Starting phenix.real_space_refine on Thu Sep 18 13:12:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vee_43171/09_2025/8vee_43171.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vee_43171/09_2025/8vee_43171.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vee_43171/09_2025/8vee_43171.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vee_43171/09_2025/8vee_43171.map" model { file = "/net/cci-nas-00/data/ceres_data/8vee_43171/09_2025/8vee_43171.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vee_43171/09_2025/8vee_43171.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.047 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 90 5.16 5 C 10593 2.51 5 N 2958 2.21 5 O 3408 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17049 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 3791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3791 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 13, 'TRANS': 471} Chain breaks: 1 Chain: "H" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 991 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 803 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "C" Number of atoms: 3791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3791 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 13, 'TRANS': 471} Chain breaks: 1 Chain: "G" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 991 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "I" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 803 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "E" Number of atoms: 3791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3791 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 13, 'TRANS': 471} Chain breaks: 1 Chain: "J" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 991 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "K" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 803 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} 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: "U" 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.00, per 1000 atoms: 0.23 Number of scatterers: 17049 At special positions: 0 Unit cell: (130.54, 130.54, 146.59, 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 90 16.00 O 3408 8.00 N 2958 7.00 C 10593 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A1137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A1144 " - pdb=" SG CYS A1148 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C1137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=1.98 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.03 Simple disulfide: pdb=" SG CYS C1144 " - pdb=" SG CYS C1148 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS E1137 " distance=2.03 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 278 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.05 Simple disulfide: pdb=" SG CYS E 282 " - pdb=" SG CYS E 306 " distance=2.03 Simple disulfide: pdb=" SG CYS E1144 " - pdb=" SG CYS E1148 " distance=2.02 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 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 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 U 1 " - " NAG U 2 " NAG-ASN " NAG A2001 " - " ASN A 241 " " NAG C2001 " - " ASN C 241 " " NAG E2001 " - " ASN E 241 " " NAG M 1 " - " ASN A 38 " " NAG N 1 " - " ASN A1082 " " NAG O 1 " - " ASN A1154 " " NAG P 1 " - " ASN C 38 " " NAG Q 1 " - " ASN C1082 " " NAG R 1 " - " ASN C1154 " " NAG S 1 " - " ASN E 38 " " NAG T 1 " - " ASN E1082 " " NAG U 1 " - " ASN E1154 " Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 697.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3894 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 45 sheets defined 18.4% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.642A pdb=" N THR A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.653A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.713A pdb=" N LEU A 108 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 1037 through 1056 removed outlier: 3.638A pdb=" N THR A1041 " --> pdb=" O ASP A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1126 Processing helix chain 'A' and resid 1145 through 1154 Processing helix chain 'A' and resid 1162 through 1172 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.063A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.643A pdb=" N THR C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 removed outlier: 3.653A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 114 removed outlier: 3.713A pdb=" N LEU C 108 " --> pdb=" O ASN C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 196 Processing helix chain 'C' and resid 1037 through 1057 removed outlier: 3.638A pdb=" N THR C1041 " --> pdb=" O ASP C1037 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU C1057 " --> pdb=" O ASN C1053 " (cutoff:3.500A) Processing helix chain 'C' and resid 1074 through 1126 Processing helix chain 'C' and resid 1145 through 1154 Processing helix chain 'C' and resid 1162 through 1172 Processing helix chain 'G' and resid 61 through 64 removed outlier: 4.412A pdb=" N ARG G 64 " --> pdb=" O PRO G 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 64' Processing helix chain 'I' and resid 79 through 83 removed outlier: 4.063A pdb=" N PHE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 72 removed outlier: 3.643A pdb=" N THR E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 77 removed outlier: 3.653A pdb=" N ASP E 77 " --> pdb=" O PRO E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 114 removed outlier: 3.712A pdb=" N LEU E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 196 Processing helix chain 'E' and resid 1037 through 1057 removed outlier: 3.638A pdb=" N THR E1041 " --> pdb=" O ASP E1037 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU E1057 " --> pdb=" O ASN E1053 " (cutoff:3.500A) Processing helix chain 'E' and resid 1074 through 1126 Processing helix chain 'E' and resid 1145 through 1154 Processing helix chain 'E' and resid 1162 through 1172 Processing helix chain 'K' and resid 79 through 83 removed outlier: 4.064A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1032 through 1036 removed outlier: 4.154A pdb=" N CYS A1137 " --> pdb=" O ASP A1133 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU A1131 " --> pdb=" O GLU A1139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 27 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 52 removed outlier: 6.051A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 58 through 61 removed outlier: 6.701A pdb=" N VAL A 59 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE A 87 " --> pdb=" O ILE A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.900A pdb=" N LYS A 101 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N TRP A 235 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL A 180 " --> pdb=" O ARG A 257 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ARG A 257 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 121 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.900A pdb=" N LYS A 101 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N TRP A 235 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N VAL A 180 " --> pdb=" O PRO A 255 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 136 through 140 removed outlier: 3.575A pdb=" N THR A 136 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 165 through 170 removed outlier: 3.605A pdb=" N GLN A 212 " --> pdb=" O VAL A 205 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 282 through 284 removed outlier: 3.937A pdb=" N CYS A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 295 through 296 Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.635A pdb=" N TYR H 50 " --> pdb=" O SER H 58 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.306A pdb=" N TRP H 35A" --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.845A pdb=" N SER L 7 " --> pdb=" O THR L 22 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 53 through 54 removed outlier: 4.057A pdb=" N ARG L 53 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER L 49 " --> pdb=" O ARG L 53 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 1032 through 1036 removed outlier: 4.153A pdb=" N CYS C1137 " --> pdb=" O ASP C1133 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU C1131 " --> pdb=" O GLU C1139 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 24 through 27 Processing sheet with id=AB9, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC1, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC2, first strand: chain 'C' and resid 51 through 52 removed outlier: 5.921A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 58 through 61 removed outlier: 6.701A pdb=" N VAL C 59 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE C 87 " --> pdb=" O ILE C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.204A pdb=" N VAL C 180 " --> pdb=" O ARG C 257 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ARG C 257 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU C 121 " --> pdb=" O ALA C 258 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 100 through 102 removed outlier: 7.898A pdb=" N VAL C 180 " --> pdb=" O PRO C 255 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 165 through 170 removed outlier: 3.605A pdb=" N GLN C 212 " --> pdb=" O VAL C 205 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 282 through 284 removed outlier: 3.938A pdb=" N CYS C 282 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.559A pdb=" N LYS G 81 " --> pdb=" O THR G 68 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 57 through 59 removed outlier: 3.561A pdb=" N TYR G 50 " --> pdb=" O SER G 58 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR G 50 " --> pdb=" O TRP G 35A" (cutoff:3.500A) removed outlier: 6.306A pdb=" N TRP G 35A" --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 57 through 59 removed outlier: 3.561A pdb=" N TYR G 50 " --> pdb=" O SER G 58 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR G 50 " --> pdb=" O TRP G 35A" (cutoff:3.500A) removed outlier: 6.306A pdb=" N TRP G 35A" --> pdb=" O TYR G 50 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.845A pdb=" N SER I 7 " --> pdb=" O THR I 22 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR I 22 " --> pdb=" O SER I 7 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 53 through 54 removed outlier: 4.051A pdb=" N ARG I 53 " --> pdb=" O SER I 49 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER I 49 " --> pdb=" O ARG I 53 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR I 102 " --> pdb=" O TYR I 86 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 1032 through 1036 removed outlier: 4.153A pdb=" N CYS E1137 " --> pdb=" O ASP E1133 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU E1131 " --> pdb=" O GLU E1139 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AD6, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AD7, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AD8, first strand: chain 'E' and resid 51 through 52 removed outlier: 5.921A pdb=" N ILE E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'E' and resid 58 through 61 removed outlier: 6.702A pdb=" N VAL E 59 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE E 87 " --> pdb=" O ILE E 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'E' and resid 118 through 122 removed outlier: 3.610A pdb=" N GLU E 121 " --> pdb=" O ALA E 258 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ARG E 257 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL E 180 " --> pdb=" O ARG E 257 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N VAL E 180 " --> pdb=" O PRO E 255 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 118 through 122 removed outlier: 3.610A pdb=" N GLU E 121 " --> pdb=" O ALA E 258 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ARG E 257 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL E 180 " --> pdb=" O ARG E 257 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 165 through 170 removed outlier: 3.605A pdb=" N GLN E 212 " --> pdb=" O VAL E 205 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 282 through 284 removed outlier: 3.937A pdb=" N CYS E 282 " --> pdb=" O ILE E 289 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.839A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR J 50 " --> pdb=" O TRP J 35A" (cutoff:3.500A) removed outlier: 6.306A pdb=" N TRP J 35A" --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.839A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR J 50 " --> pdb=" O TRP J 35A" (cutoff:3.500A) removed outlier: 6.306A pdb=" N TRP J 35A" --> pdb=" O TYR J 50 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.845A pdb=" N SER K 7 " --> pdb=" O THR K 22 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR K 22 " --> pdb=" O SER K 7 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 45 through 46 removed outlier: 3.741A pdb=" N THR K 102 " --> pdb=" O TYR K 86 " (cutoff:3.500A) 667 hydrogen bonds defined for protein. 1812 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: 3.28 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2871 1.30 - 1.43: 4653 1.43 - 1.56: 9725 1.56 - 1.69: 4 1.69 - 1.81: 129 Bond restraints: 17382 Sorted by residual: bond pdb=" C ASP E 232 " pdb=" N PHE E 233 " ideal model delta sigma weight residual 1.331 1.466 -0.136 1.34e-02 5.57e+03 1.03e+02 bond pdb=" N ARG A 140 " pdb=" CA ARG A 140 " ideal model delta sigma weight residual 1.455 1.511 -0.056 1.21e-02 6.83e+03 2.12e+01 bond pdb=" C TYR E 98 " pdb=" O TYR E 98 " ideal model delta sigma weight residual 1.234 1.173 0.060 1.31e-02 5.83e+03 2.11e+01 bond pdb=" N ARG E 140 " pdb=" CA ARG E 140 " ideal model delta sigma weight residual 1.461 1.517 -0.056 1.38e-02 5.25e+03 1.66e+01 bond pdb=" N ILE E 48 " pdb=" CA ILE E 48 " ideal model delta sigma weight residual 1.460 1.488 -0.028 7.30e-03 1.88e+04 1.49e+01 ... (remaining 17377 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.66: 23264 4.66 - 9.33: 228 9.33 - 13.99: 20 13.99 - 18.65: 1 18.65 - 23.32: 1 Bond angle restraints: 23514 Sorted by residual: angle pdb=" CA SER C 144 " pdb=" CB SER C 144 " pdb=" OG SER C 144 " ideal model delta sigma weight residual 111.10 134.42 -23.32 2.00e+00 2.50e-01 1.36e+02 angle pdb=" C TYR H 99 " pdb=" CA TYR H 99 " pdb=" CB TYR H 99 " ideal model delta sigma weight residual 110.79 95.85 14.94 1.63e+00 3.76e-01 8.41e+01 angle pdb=" C CYS C 139 " pdb=" CA CYS C 139 " pdb=" CB CYS C 139 " ideal model delta sigma weight residual 110.62 123.44 -12.82 1.51e+00 4.39e-01 7.21e+01 angle pdb=" N GLU H 100J" pdb=" CA GLU H 100J" pdb=" C GLU H 100J" ideal model delta sigma weight residual 113.61 101.91 11.70 1.50e+00 4.44e-01 6.08e+01 angle pdb=" CA TYR E 98 " pdb=" C TYR E 98 " pdb=" O TYR E 98 " ideal model delta sigma weight residual 120.88 112.32 8.56 1.12e+00 7.97e-01 5.84e+01 ... (remaining 23509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.40: 9488 16.40 - 32.80: 854 32.80 - 49.21: 221 49.21 - 65.61: 35 65.61 - 82.01: 28 Dihedral angle restraints: 10626 sinusoidal: 4506 harmonic: 6120 Sorted by residual: dihedral pdb=" C TYR H 99 " pdb=" N TYR H 99 " pdb=" CA TYR H 99 " pdb=" CB TYR H 99 " ideal model delta harmonic sigma weight residual -122.60 -104.68 -17.92 0 2.50e+00 1.60e-01 5.14e+01 dihedral pdb=" C ASP J 100 " pdb=" N ASP J 100 " pdb=" CA ASP J 100 " pdb=" CB ASP J 100 " ideal model delta harmonic sigma weight residual -122.60 -105.40 -17.20 0 2.50e+00 1.60e-01 4.73e+01 dihedral pdb=" N ASN C 241 " pdb=" C ASN C 241 " pdb=" CA ASN C 241 " pdb=" CB ASN C 241 " ideal model delta harmonic sigma weight residual 122.80 138.42 -15.62 0 2.50e+00 1.60e-01 3.90e+01 ... (remaining 10623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.202: 2537 0.202 - 0.404: 65 0.404 - 0.606: 4 0.606 - 0.808: 0 0.808 - 1.011: 1 Chirality restraints: 2607 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.34e+02 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN A1154 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.39 -1.01 2.00e-01 2.50e+01 2.55e+01 chirality pdb=" C1 NAG E2001 " pdb=" ND2 ASN E 241 " pdb=" C2 NAG E2001 " pdb=" O5 NAG E2001 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 8.95e+00 ... (remaining 2604 not shown) Planarity restraints: 3063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 2 " 0.358 2.00e-02 2.50e+03 3.09e-01 1.19e+03 pdb=" C7 NAG S 2 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG S 2 " 0.114 2.00e-02 2.50e+03 pdb=" N2 NAG S 2 " -0.548 2.00e-02 2.50e+03 pdb=" O7 NAG S 2 " 0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 1 " 0.347 2.00e-02 2.50e+03 3.00e-01 1.12e+03 pdb=" C7 NAG S 1 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG S 1 " 0.133 2.00e-02 2.50e+03 pdb=" N2 NAG S 1 " -0.535 2.00e-02 2.50e+03 pdb=" O7 NAG S 1 " 0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 2 " -0.334 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG O 2 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG O 2 " -0.139 2.00e-02 2.50e+03 pdb=" N2 NAG O 2 " 0.518 2.00e-02 2.50e+03 pdb=" O7 NAG O 2 " -0.121 2.00e-02 2.50e+03 ... (remaining 3060 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3621 2.79 - 3.32: 14202 3.32 - 3.84: 28357 3.84 - 4.37: 32613 4.37 - 4.90: 57188 Nonbonded interactions: 135981 Sorted by model distance: nonbonded pdb=" N TYR E 98 " pdb=" O TYR E 98 " model vdw 2.260 2.496 nonbonded pdb=" OE2 GLU G 101 " pdb=" OH TYR I 36 " model vdw 2.315 3.040 nonbonded pdb=" O SER I 50 " pdb=" OG SER I 50 " model vdw 2.317 3.040 nonbonded pdb=" O SER L 50 " pdb=" OG SER L 50 " model vdw 2.318 3.040 nonbonded pdb=" OG SER E 207 " pdb=" OD2 ASP E 242 " model vdw 2.348 3.040 ... (remaining 135976 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 'C' selection = chain 'E' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.450 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 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 : 0.007 0.136 17427 Z= 0.426 Angle : 1.234 23.317 23625 Z= 0.797 Chirality : 0.077 1.011 2607 Planarity : 0.016 0.309 3051 Dihedral : 13.741 82.009 6660 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 1.03 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.16), residues: 2130 helix: 0.43 (0.27), residues: 321 sheet: 0.84 (0.25), residues: 474 loop : -1.71 (0.14), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E1170 TYR 0.036 0.003 TYR E1094 PHE 0.029 0.002 PHE E1009 TRP 0.044 0.002 TRP K 35 HIS 0.008 0.001 HIS A1142 Details of bonding type rmsd covalent geometry : bond 0.00632 (17382) covalent geometry : angle 1.21637 (23514) SS BOND : bond 0.01150 ( 24) SS BOND : angle 2.41924 ( 48) hydrogen bonds : bond 0.19544 ( 615) hydrogen bonds : angle 8.56761 ( 1812) link_BETA1-4 : bond 0.01491 ( 9) link_BETA1-4 : angle 2.44416 ( 27) link_NAG-ASN : bond 0.05741 ( 12) link_NAG-ASN : angle 4.48253 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 439 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1010 ILE cc_start: 0.8287 (mt) cc_final: 0.7918 (mm) REVERT: A 1052 LEU cc_start: 0.8099 (mt) cc_final: 0.7739 (mm) REVERT: A 1108 ILE cc_start: 0.8075 (mt) cc_final: 0.7783 (mt) REVERT: H 58 SER cc_start: 0.8361 (t) cc_final: 0.7850 (m) REVERT: H 79 SER cc_start: 0.8638 (m) cc_final: 0.8225 (t) REVERT: C 47 ASN cc_start: 0.8102 (p0) cc_final: 0.7887 (p0) REVERT: C 243 THR cc_start: 0.7818 (m) cc_final: 0.7492 (m) REVERT: C 1055 LEU cc_start: 0.8100 (mt) cc_final: 0.7889 (mp) REVERT: C 1115 MET cc_start: 0.8838 (tpp) cc_final: 0.8637 (tpt) REVERT: G 100 VAL cc_start: 0.8160 (t) cc_final: 0.7959 (m) REVERT: I 32 ASP cc_start: 0.6916 (m-30) cc_final: 0.6612 (m-30) REVERT: J 79 SER cc_start: 0.8521 (m) cc_final: 0.8232 (t) REVERT: J 100 PHE cc_start: 0.8293 (m-10) cc_final: 0.7930 (m-80) REVERT: K 36 TYR cc_start: 0.7195 (m-80) cc_final: 0.6990 (m-80) REVERT: K 47 LEU cc_start: 0.7674 (mt) cc_final: 0.7315 (mt) outliers start: 0 outliers final: 0 residues processed: 439 average time/residue: 0.1358 time to fit residues: 87.6036 Evaluate side-chains 290 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 0.0000 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.4980 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 156 ASN A 323 ASN A1053 ASN A1095 ASN L 3 GLN L 45 GLN C 75 GLN C 227 GLN C 297 ASN C 323 ASN I 3 GLN I 31 ASN I 45 GLN E 323 ASN K 3 GLN K 45 GLN K 92 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.159974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.121056 restraints weight = 20366.140| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.19 r_work: 0.3302 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17427 Z= 0.166 Angle : 0.640 13.496 23625 Z= 0.327 Chirality : 0.044 0.282 2607 Planarity : 0.005 0.057 3051 Dihedral : 6.086 59.761 2784 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.86 % Allowed : 9.27 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.17), residues: 2130 helix: 2.21 (0.28), residues: 324 sheet: 0.77 (0.24), residues: 510 loop : -1.38 (0.15), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1127 TYR 0.019 0.002 TYR J 35 PHE 0.031 0.002 PHE C1009 TRP 0.014 0.002 TRP J 47 HIS 0.004 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00384 (17382) covalent geometry : angle 0.63012 (23514) SS BOND : bond 0.00849 ( 24) SS BOND : angle 1.52080 ( 48) hydrogen bonds : bond 0.04797 ( 615) hydrogen bonds : angle 5.74325 ( 1812) link_BETA1-4 : bond 0.00562 ( 9) link_BETA1-4 : angle 1.73117 ( 27) link_NAG-ASN : bond 0.00619 ( 12) link_NAG-ASN : angle 1.95789 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 298 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ILE cc_start: 0.8329 (mm) cc_final: 0.8128 (mm) REVERT: A 211 GLN cc_start: 0.7337 (pt0) cc_final: 0.6710 (pt0) REVERT: A 1047 GLN cc_start: 0.8465 (mt0) cc_final: 0.8210 (mt0) REVERT: A 1068 ASN cc_start: 0.8624 (t0) cc_final: 0.8366 (t0) REVERT: L 32 ASP cc_start: 0.6883 (m-30) cc_final: 0.6572 (m-30) REVERT: C 47 ASN cc_start: 0.8485 (p0) cc_final: 0.8236 (p0) REVERT: C 227 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6806 (mt0) REVERT: C 243 THR cc_start: 0.8150 (m) cc_final: 0.7937 (m) REVERT: C 1024 PHE cc_start: 0.8069 (m-80) cc_final: 0.7822 (m-10) REVERT: G 25 SER cc_start: 0.8158 (t) cc_final: 0.7596 (p) REVERT: I 63 SER cc_start: 0.6121 (t) cc_final: 0.5179 (p) REVERT: E 31 GLU cc_start: 0.7487 (tt0) cc_final: 0.7166 (tt0) REVERT: E 140 ARG cc_start: 0.7152 (ttm-80) cc_final: 0.6848 (ttm-80) REVERT: E 183 ILE cc_start: 0.8284 (mm) cc_final: 0.8047 (mm) REVERT: E 211 GLN cc_start: 0.7742 (pt0) cc_final: 0.6798 (pt0) REVERT: E 212 GLN cc_start: 0.7971 (tp40) cc_final: 0.7760 (tp40) REVERT: E 321 MET cc_start: 0.8503 (ptm) cc_final: 0.8302 (ptp) REVERT: J 97 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.8506 (m-80) REVERT: J 100 PHE cc_start: 0.8573 (m-10) cc_final: 0.8169 (m-80) REVERT: K 32 ASP cc_start: 0.6936 (m-30) cc_final: 0.6656 (m-30) REVERT: K 47 LEU cc_start: 0.7612 (mt) cc_final: 0.7350 (mt) outliers start: 34 outliers final: 20 residues processed: 320 average time/residue: 0.1408 time to fit residues: 66.7058 Evaluate side-chains 270 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 248 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 1071 THR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 227 GLN Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 1110 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 97 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 50 optimal weight: 7.9990 chunk 30 optimal weight: 0.1980 chunk 15 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 152 optimal weight: 6.9990 chunk 197 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 227 GLN C1053 ASN I 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.151291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.112006 restraints weight = 20860.898| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.10 r_work: 0.3191 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 17427 Z= 0.287 Angle : 0.706 10.762 23625 Z= 0.365 Chirality : 0.046 0.229 2607 Planarity : 0.005 0.050 3051 Dihedral : 5.927 51.642 2784 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.40 % Allowed : 12.45 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.17), residues: 2130 helix: 2.09 (0.28), residues: 330 sheet: 0.64 (0.23), residues: 558 loop : -1.51 (0.15), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1127 TYR 0.029 0.003 TYR G 35 PHE 0.031 0.003 PHE C1009 TRP 0.016 0.002 TRP E 235 HIS 0.010 0.002 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00694 (17382) covalent geometry : angle 0.69592 (23514) SS BOND : bond 0.00605 ( 24) SS BOND : angle 1.99005 ( 48) hydrogen bonds : bond 0.05300 ( 615) hydrogen bonds : angle 5.31674 ( 1812) link_BETA1-4 : bond 0.00443 ( 9) link_BETA1-4 : angle 1.73256 ( 27) link_NAG-ASN : bond 0.00309 ( 12) link_NAG-ASN : angle 1.88184 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 271 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ILE cc_start: 0.8435 (mm) cc_final: 0.8215 (mm) REVERT: A 211 GLN cc_start: 0.7444 (pt0) cc_final: 0.6742 (pt0) REVERT: A 1052 LEU cc_start: 0.8508 (mt) cc_final: 0.8119 (mp) REVERT: A 1066 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7247 (mt) REVERT: A 1116 ASP cc_start: 0.7870 (m-30) cc_final: 0.7649 (m-30) REVERT: A 1143 LYS cc_start: 0.7129 (ttmm) cc_final: 0.6856 (ttpt) REVERT: H 21 THR cc_start: 0.8131 (p) cc_final: 0.7828 (t) REVERT: L 32 ASP cc_start: 0.7185 (m-30) cc_final: 0.6974 (m-30) REVERT: L 63 SER cc_start: 0.6404 (t) cc_final: 0.5618 (p) REVERT: C 47 ASN cc_start: 0.8715 (p0) cc_final: 0.8351 (p0) REVERT: C 114 GLU cc_start: 0.7527 (pt0) cc_final: 0.7286 (pt0) REVERT: C 194 LYS cc_start: 0.7572 (tmtt) cc_final: 0.7322 (tmmt) REVERT: C 1024 PHE cc_start: 0.8437 (m-80) cc_final: 0.8048 (m-10) REVERT: C 1143 LYS cc_start: 0.7217 (ttmm) cc_final: 0.6922 (ttpt) REVERT: G 21 THR cc_start: 0.8317 (p) cc_final: 0.7905 (t) REVERT: G 25 SER cc_start: 0.8182 (t) cc_final: 0.7691 (p) REVERT: G 69 ILE cc_start: 0.7572 (tt) cc_final: 0.7295 (tt) REVERT: G 97 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.8458 (m-80) REVERT: I 32 ASP cc_start: 0.7076 (m-30) cc_final: 0.6671 (m-30) REVERT: E 15 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8227 (mt) REVERT: E 31 GLU cc_start: 0.7460 (tt0) cc_final: 0.7229 (tt0) REVERT: E 115 SER cc_start: 0.8295 (p) cc_final: 0.8058 (t) REVERT: E 140 ARG cc_start: 0.7625 (ttm-80) cc_final: 0.7405 (ttm-80) REVERT: E 211 GLN cc_start: 0.8009 (pt0) cc_final: 0.6962 (pt0) REVERT: J 21 THR cc_start: 0.8113 (p) cc_final: 0.7791 (t) REVERT: K 32 ASP cc_start: 0.7464 (m-30) cc_final: 0.7217 (m-30) REVERT: K 53 ARG cc_start: 0.7638 (mtt90) cc_final: 0.7290 (mtt180) outliers start: 62 outliers final: 43 residues processed: 318 average time/residue: 0.1192 time to fit residues: 58.2178 Evaluate side-chains 278 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 232 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1071 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1077 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 97 PHE Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 1067 ASP Chi-restraints excluded: chain E residue 1071 THR Chi-restraints excluded: chain E residue 1110 LEU Chi-restraints excluded: chain E residue 1117 LYS Chi-restraints excluded: chain K residue 104 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 81 optimal weight: 0.5980 chunk 74 optimal weight: 6.9990 chunk 188 optimal weight: 0.5980 chunk 173 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 170 optimal weight: 0.5980 chunk 164 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1060 ASN C 63 GLN C1060 ASN E1060 ASN E1125 GLN K 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.158895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.120622 restraints weight = 20557.968| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.02 r_work: 0.3255 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17427 Z= 0.137 Angle : 0.603 11.207 23625 Z= 0.305 Chirality : 0.043 0.396 2607 Planarity : 0.004 0.047 3051 Dihedral : 5.393 54.063 2784 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.36 % Allowed : 15.13 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.17), residues: 2130 helix: 2.64 (0.28), residues: 324 sheet: 0.76 (0.23), residues: 558 loop : -1.43 (0.15), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 230 TYR 0.016 0.001 TYR G 35 PHE 0.021 0.002 PHE C 246 TRP 0.007 0.001 TRP L 35 HIS 0.004 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00321 (17382) covalent geometry : angle 0.58206 (23514) SS BOND : bond 0.00408 ( 24) SS BOND : angle 2.62548 ( 48) hydrogen bonds : bond 0.04144 ( 615) hydrogen bonds : angle 4.90877 ( 1812) link_BETA1-4 : bond 0.00400 ( 9) link_BETA1-4 : angle 1.57787 ( 27) link_NAG-ASN : bond 0.00297 ( 12) link_NAG-ASN : angle 2.48675 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 245 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 GLN cc_start: 0.7547 (pt0) cc_final: 0.6860 (pt0) REVERT: A 1052 LEU cc_start: 0.8417 (mt) cc_final: 0.8031 (mp) REVERT: A 1066 ILE cc_start: 0.8164 (pt) cc_final: 0.7165 (mt) REVERT: A 1127 ARG cc_start: 0.7332 (ttm-80) cc_final: 0.6976 (tpp-160) REVERT: A 1143 LYS cc_start: 0.7028 (ttmm) cc_final: 0.6793 (ttpt) REVERT: A 1163 ARG cc_start: 0.8248 (ttt90) cc_final: 0.7760 (tpt-90) REVERT: H 21 THR cc_start: 0.8086 (p) cc_final: 0.7830 (t) REVERT: H 25 SER cc_start: 0.8080 (t) cc_final: 0.7505 (p) REVERT: L 32 ASP cc_start: 0.7230 (m-30) cc_final: 0.6945 (m-30) REVERT: L 63 SER cc_start: 0.6388 (t) cc_final: 0.5652 (p) REVERT: C 47 ASN cc_start: 0.8608 (p0) cc_final: 0.8282 (p0) REVERT: C 114 GLU cc_start: 0.7276 (pt0) cc_final: 0.7064 (pt0) REVERT: C 115 SER cc_start: 0.8414 (p) cc_final: 0.8114 (t) REVERT: C 194 LYS cc_start: 0.7707 (tmtt) cc_final: 0.7496 (tmmt) REVERT: C 264 LYS cc_start: 0.8164 (tptt) cc_final: 0.7611 (mmtm) REVERT: C 1024 PHE cc_start: 0.8361 (m-80) cc_final: 0.8120 (m-80) REVERT: G 21 THR cc_start: 0.8144 (p) cc_final: 0.7812 (t) REVERT: G 25 SER cc_start: 0.8221 (t) cc_final: 0.7775 (p) REVERT: G 69 ILE cc_start: 0.7514 (tt) cc_final: 0.7226 (tt) REVERT: G 97 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8582 (m-80) REVERT: I 32 ASP cc_start: 0.7191 (m-30) cc_final: 0.6779 (m-30) REVERT: E 15 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8175 (mp) REVERT: E 140 ARG cc_start: 0.7709 (ttm-80) cc_final: 0.7482 (ttm-80) REVERT: E 211 GLN cc_start: 0.7949 (pt0) cc_final: 0.6653 (pt0) REVERT: E 246 PHE cc_start: 0.7783 (m-80) cc_final: 0.7579 (m-10) REVERT: J 21 THR cc_start: 0.8020 (p) cc_final: 0.7763 (t) REVERT: J 97 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.8574 (m-80) REVERT: K 32 ASP cc_start: 0.7560 (m-30) cc_final: 0.7270 (m-30) outliers start: 43 outliers final: 26 residues processed: 274 average time/residue: 0.1264 time to fit residues: 52.7066 Evaluate side-chains 263 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 234 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1060 ASN Chi-restraints excluded: chain A residue 1071 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1055 LEU Chi-restraints excluded: chain C residue 1077 ILE Chi-restraints excluded: chain C residue 1110 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 97 PHE Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 1071 THR Chi-restraints excluded: chain E residue 1074 GLU Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 97 PHE Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 25 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 170 optimal weight: 0.9980 chunk 207 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1060 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.150090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.113117 restraints weight = 20489.854| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.06 r_work: 0.3105 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 17427 Z= 0.330 Angle : 0.739 10.189 23625 Z= 0.376 Chirality : 0.049 0.699 2607 Planarity : 0.005 0.046 3051 Dihedral : 6.366 83.927 2784 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.45 % Allowed : 15.57 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.17), residues: 2130 helix: 2.02 (0.27), residues: 330 sheet: 0.35 (0.22), residues: 570 loop : -1.56 (0.15), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E1124 TYR 0.025 0.003 TYR G 35 PHE 0.025 0.003 PHE H 78 TRP 0.016 0.002 TRP E 235 HIS 0.010 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00797 (17382) covalent geometry : angle 0.71968 (23514) SS BOND : bond 0.00620 ( 24) SS BOND : angle 2.88410 ( 48) hydrogen bonds : bond 0.05191 ( 615) hydrogen bonds : angle 5.15352 ( 1812) link_BETA1-4 : bond 0.00283 ( 9) link_BETA1-4 : angle 1.82938 ( 27) link_NAG-ASN : bond 0.00442 ( 12) link_NAG-ASN : angle 2.50019 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 250 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ILE cc_start: 0.8691 (mm) cc_final: 0.8431 (mt) REVERT: A 211 GLN cc_start: 0.7583 (pt0) cc_final: 0.6835 (pt0) REVERT: A 321 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8418 (ptm) REVERT: A 1052 LEU cc_start: 0.8463 (mt) cc_final: 0.8090 (mp) REVERT: A 1127 ARG cc_start: 0.7595 (ttm-80) cc_final: 0.7116 (tpp-160) REVERT: A 1143 LYS cc_start: 0.7335 (ttmm) cc_final: 0.7099 (ttpt) REVERT: A 1164 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7428 (tp30) REVERT: H 21 THR cc_start: 0.8112 (p) cc_final: 0.7823 (t) REVERT: H 25 SER cc_start: 0.8026 (t) cc_final: 0.7463 (p) REVERT: L 31 ASN cc_start: 0.7450 (OUTLIER) cc_final: 0.6659 (t0) REVERT: L 32 ASP cc_start: 0.7326 (m-30) cc_final: 0.7045 (m-30) REVERT: L 63 SER cc_start: 0.6716 (t) cc_final: 0.5928 (p) REVERT: C 114 GLU cc_start: 0.7563 (pt0) cc_final: 0.7317 (pt0) REVERT: C 115 SER cc_start: 0.8512 (p) cc_final: 0.8089 (t) REVERT: C 194 LYS cc_start: 0.7768 (tmtt) cc_final: 0.7525 (tmmt) REVERT: C 204 THR cc_start: 0.7897 (m) cc_final: 0.7677 (m) REVERT: C 1024 PHE cc_start: 0.8561 (m-80) cc_final: 0.8080 (m-80) REVERT: G 21 THR cc_start: 0.8091 (p) cc_final: 0.7694 (t) REVERT: G 25 SER cc_start: 0.8235 (t) cc_final: 0.7778 (p) REVERT: G 69 ILE cc_start: 0.7617 (tt) cc_final: 0.7349 (tt) REVERT: G 97 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.8238 (m-80) REVERT: I 32 ASP cc_start: 0.7212 (m-30) cc_final: 0.6748 (m-30) REVERT: E 211 GLN cc_start: 0.7808 (pt0) cc_final: 0.6708 (pt0) REVERT: J 21 THR cc_start: 0.8008 (p) cc_final: 0.7691 (t) REVERT: J 97 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.8593 (m-80) REVERT: K 32 ASP cc_start: 0.7469 (m-30) cc_final: 0.7127 (m-30) REVERT: K 94 TYR cc_start: 0.6721 (m-80) cc_final: 0.6253 (m-80) outliers start: 63 outliers final: 50 residues processed: 295 average time/residue: 0.1182 time to fit residues: 53.6685 Evaluate side-chains 292 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 238 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1071 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1055 LEU Chi-restraints excluded: chain C residue 1059 THR Chi-restraints excluded: chain C residue 1071 THR Chi-restraints excluded: chain C residue 1131 GLU Chi-restraints excluded: chain C residue 1165 GLU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 97 PHE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 1067 ASP Chi-restraints excluded: chain E residue 1071 THR Chi-restraints excluded: chain E residue 1074 GLU Chi-restraints excluded: chain E residue 1110 LEU Chi-restraints excluded: chain E residue 1117 LYS Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 97 PHE Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 3 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 0.0980 chunk 104 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 HIS E 156 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.154126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.115612 restraints weight = 20299.859| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.11 r_work: 0.3197 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17427 Z= 0.121 Angle : 0.587 13.599 23625 Z= 0.295 Chirality : 0.044 0.536 2607 Planarity : 0.003 0.045 3051 Dihedral : 5.287 50.896 2784 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.25 % Allowed : 17.54 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.17), residues: 2130 helix: 2.71 (0.28), residues: 324 sheet: 0.45 (0.22), residues: 558 loop : -1.49 (0.15), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 230 TYR 0.018 0.001 TYR J 50 PHE 0.020 0.001 PHE C 246 TRP 0.008 0.001 TRP J 47 HIS 0.003 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00275 (17382) covalent geometry : angle 0.56561 (23514) SS BOND : bond 0.00340 ( 24) SS BOND : angle 1.97021 ( 48) hydrogen bonds : bond 0.04025 ( 615) hydrogen bonds : angle 4.78274 ( 1812) link_BETA1-4 : bond 0.00425 ( 9) link_BETA1-4 : angle 1.60126 ( 27) link_NAG-ASN : bond 0.01069 ( 12) link_NAG-ASN : angle 3.17897 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 256 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLN cc_start: 0.7884 (pt0) cc_final: 0.7187 (pt0) REVERT: A 264 LYS cc_start: 0.8233 (tptt) cc_final: 0.7481 (mmtm) REVERT: A 1052 LEU cc_start: 0.8363 (mt) cc_final: 0.7964 (mp) REVERT: A 1127 ARG cc_start: 0.7407 (ttm-80) cc_final: 0.6756 (tpp-160) REVERT: A 1128 GLU cc_start: 0.7345 (mt-10) cc_final: 0.7109 (mt-10) REVERT: A 1143 LYS cc_start: 0.7273 (ttmm) cc_final: 0.6950 (ttpt) REVERT: H 21 THR cc_start: 0.8078 (p) cc_final: 0.7809 (t) REVERT: H 25 SER cc_start: 0.7997 (t) cc_final: 0.7426 (p) REVERT: H 39 GLN cc_start: 0.7640 (tp40) cc_final: 0.7014 (tp40) REVERT: L 32 ASP cc_start: 0.7188 (m-30) cc_final: 0.6966 (m-30) REVERT: L 63 SER cc_start: 0.6718 (t) cc_final: 0.5927 (p) REVERT: C 115 SER cc_start: 0.8334 (p) cc_final: 0.7960 (t) REVERT: C 194 LYS cc_start: 0.7718 (tmtt) cc_final: 0.7484 (tmmt) REVERT: C 264 LYS cc_start: 0.8246 (tptt) cc_final: 0.7585 (mmtm) REVERT: C 1024 PHE cc_start: 0.8506 (m-80) cc_final: 0.8000 (m-10) REVERT: C 1131 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6958 (pt0) REVERT: G 21 THR cc_start: 0.8074 (p) cc_final: 0.7700 (t) REVERT: G 25 SER cc_start: 0.8181 (t) cc_final: 0.7720 (p) REVERT: G 69 ILE cc_start: 0.7537 (tt) cc_final: 0.7285 (tt) REVERT: G 97 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8491 (m-80) REVERT: E 156 ASN cc_start: 0.7790 (OUTLIER) cc_final: 0.7466 (m-40) REVERT: E 183 ILE cc_start: 0.8192 (mm) cc_final: 0.7960 (mm) REVERT: E 1052 LEU cc_start: 0.8286 (mt) cc_final: 0.8024 (mp) REVERT: E 1143 LYS cc_start: 0.7615 (ttmm) cc_final: 0.7401 (ttpt) REVERT: E 1163 ARG cc_start: 0.8076 (ttt90) cc_final: 0.7849 (tpt-90) REVERT: J 21 THR cc_start: 0.8002 (p) cc_final: 0.7698 (t) REVERT: J 97 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8493 (m-80) REVERT: K 32 ASP cc_start: 0.7476 (m-30) cc_final: 0.7104 (m-30) outliers start: 41 outliers final: 30 residues processed: 282 average time/residue: 0.1194 time to fit residues: 51.2407 Evaluate side-chains 275 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 241 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1056 ILE Chi-restraints excluded: chain A residue 1071 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 1055 LEU Chi-restraints excluded: chain C residue 1071 THR Chi-restraints excluded: chain C residue 1077 ILE Chi-restraints excluded: chain C residue 1110 LEU Chi-restraints excluded: chain C residue 1131 GLU Chi-restraints excluded: chain C residue 1165 GLU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 97 PHE Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 1071 THR Chi-restraints excluded: chain E residue 1074 GLU Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 97 PHE Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 41 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS C 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.152437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.113709 restraints weight = 20374.629| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.11 r_work: 0.3179 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17427 Z= 0.150 Angle : 0.594 13.450 23625 Z= 0.300 Chirality : 0.044 0.591 2607 Planarity : 0.003 0.042 3051 Dihedral : 5.287 59.833 2784 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.74 % Allowed : 17.11 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.17), residues: 2130 helix: 2.77 (0.28), residues: 324 sheet: 0.40 (0.22), residues: 558 loop : -1.46 (0.15), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E1124 TYR 0.027 0.002 TYR E 196 PHE 0.023 0.001 PHE C 246 TRP 0.014 0.001 TRP J 47 HIS 0.004 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00353 (17382) covalent geometry : angle 0.57284 (23514) SS BOND : bond 0.00383 ( 24) SS BOND : angle 2.01874 ( 48) hydrogen bonds : bond 0.04110 ( 615) hydrogen bonds : angle 4.70052 ( 1812) link_BETA1-4 : bond 0.00310 ( 9) link_BETA1-4 : angle 1.60635 ( 27) link_NAG-ASN : bond 0.01110 ( 12) link_NAG-ASN : angle 3.15611 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 249 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLN cc_start: 0.7888 (pt0) cc_final: 0.7122 (pt0) REVERT: A 264 LYS cc_start: 0.8272 (tptt) cc_final: 0.7490 (mmtm) REVERT: A 278 CYS cc_start: 0.6073 (OUTLIER) cc_final: 0.5717 (p) REVERT: A 1066 ILE cc_start: 0.8191 (pt) cc_final: 0.7196 (mt) REVERT: A 1127 ARG cc_start: 0.7536 (ttm-80) cc_final: 0.6959 (tpp-160) REVERT: A 1143 LYS cc_start: 0.7371 (ttmm) cc_final: 0.7033 (ttpt) REVERT: H 21 THR cc_start: 0.8075 (p) cc_final: 0.7817 (t) REVERT: H 25 SER cc_start: 0.8027 (t) cc_final: 0.7457 (p) REVERT: L 32 ASP cc_start: 0.7173 (m-30) cc_final: 0.6922 (m-30) REVERT: L 63 SER cc_start: 0.6748 (t) cc_final: 0.5977 (p) REVERT: C 115 SER cc_start: 0.8306 (p) cc_final: 0.7875 (t) REVERT: C 194 LYS cc_start: 0.7717 (tmtt) cc_final: 0.7500 (tmmt) REVERT: C 264 LYS cc_start: 0.8253 (tptt) cc_final: 0.7589 (mmtm) REVERT: C 1024 PHE cc_start: 0.8515 (m-80) cc_final: 0.8020 (m-10) REVERT: C 1131 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6997 (pt0) REVERT: C 1132 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7766 (mt-10) REVERT: G 21 THR cc_start: 0.8077 (p) cc_final: 0.7713 (t) REVERT: G 25 SER cc_start: 0.8245 (t) cc_final: 0.7771 (p) REVERT: G 69 ILE cc_start: 0.7535 (tt) cc_final: 0.7279 (tt) REVERT: G 97 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8415 (m-80) REVERT: I 32 ASP cc_start: 0.6891 (m-30) cc_final: 0.6513 (m-30) REVERT: E 156 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7636 (m110) REVERT: E 183 ILE cc_start: 0.8256 (mm) cc_final: 0.8024 (mm) REVERT: E 194 LYS cc_start: 0.7806 (tmtt) cc_final: 0.7203 (tmmt) REVERT: E 246 PHE cc_start: 0.8113 (m-80) cc_final: 0.7859 (m-10) REVERT: E 1143 LYS cc_start: 0.7664 (ttmm) cc_final: 0.7459 (ttpt) REVERT: E 1163 ARG cc_start: 0.8086 (ttt90) cc_final: 0.7849 (tpt-90) REVERT: J 21 THR cc_start: 0.7958 (p) cc_final: 0.7668 (t) REVERT: J 97 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.8537 (m-80) REVERT: K 32 ASP cc_start: 0.7465 (m-30) cc_final: 0.7085 (m-30) outliers start: 50 outliers final: 36 residues processed: 284 average time/residue: 0.1184 time to fit residues: 51.5938 Evaluate side-chains 279 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 238 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 1056 ILE Chi-restraints excluded: chain A residue 1071 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 1055 LEU Chi-restraints excluded: chain C residue 1071 THR Chi-restraints excluded: chain C residue 1077 ILE Chi-restraints excluded: chain C residue 1110 LEU Chi-restraints excluded: chain C residue 1131 GLU Chi-restraints excluded: chain C residue 1165 GLU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 97 PHE Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 1067 ASP Chi-restraints excluded: chain E residue 1071 THR Chi-restraints excluded: chain E residue 1074 GLU Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 97 PHE Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 163 optimal weight: 0.0980 chunk 72 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 173 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 61 optimal weight: 0.0040 chunk 6 optimal weight: 0.3980 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 156 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.155303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.116677 restraints weight = 20351.402| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.12 r_work: 0.3221 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17427 Z= 0.103 Angle : 0.549 13.574 23625 Z= 0.277 Chirality : 0.043 0.557 2607 Planarity : 0.003 0.045 3051 Dihedral : 4.985 55.591 2784 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.19 % Allowed : 17.93 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.17), residues: 2130 helix: 3.08 (0.27), residues: 327 sheet: 0.37 (0.22), residues: 576 loop : -1.33 (0.15), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E1124 TYR 0.021 0.001 TYR E 196 PHE 0.021 0.001 PHE C 246 TRP 0.023 0.001 TRP J 47 HIS 0.003 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00230 (17382) covalent geometry : angle 0.52882 (23514) SS BOND : bond 0.00289 ( 24) SS BOND : angle 1.65944 ( 48) hydrogen bonds : bond 0.03707 ( 615) hydrogen bonds : angle 4.52672 ( 1812) link_BETA1-4 : bond 0.00382 ( 9) link_BETA1-4 : angle 1.54917 ( 27) link_NAG-ASN : bond 0.00989 ( 12) link_NAG-ASN : angle 3.06223 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 251 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLN cc_start: 0.7880 (pt0) cc_final: 0.7137 (pt0) REVERT: A 264 LYS cc_start: 0.8194 (tptt) cc_final: 0.7397 (mmtm) REVERT: A 278 CYS cc_start: 0.5903 (OUTLIER) cc_final: 0.5573 (p) REVERT: A 1052 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7971 (mp) REVERT: A 1066 ILE cc_start: 0.8148 (pt) cc_final: 0.7166 (mt) REVERT: A 1143 LYS cc_start: 0.7428 (ttmm) cc_final: 0.7087 (ttpt) REVERT: H 21 THR cc_start: 0.8087 (p) cc_final: 0.7839 (t) REVERT: H 25 SER cc_start: 0.8312 (t) cc_final: 0.7676 (p) REVERT: L 32 ASP cc_start: 0.7096 (m-30) cc_final: 0.6842 (m-30) REVERT: L 63 SER cc_start: 0.6749 (t) cc_final: 0.6066 (p) REVERT: C 47 ASN cc_start: 0.8675 (p0) cc_final: 0.8134 (p0) REVERT: C 114 GLU cc_start: 0.6839 (pt0) cc_final: 0.6604 (pt0) REVERT: C 115 SER cc_start: 0.8236 (p) cc_final: 0.7825 (t) REVERT: C 194 LYS cc_start: 0.7688 (tmtt) cc_final: 0.7468 (tmmt) REVERT: C 264 LYS cc_start: 0.8179 (tptt) cc_final: 0.7559 (mmtm) REVERT: C 1024 PHE cc_start: 0.8478 (m-80) cc_final: 0.8015 (m-80) REVERT: C 1103 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7345 (mt-10) REVERT: G 25 SER cc_start: 0.8211 (t) cc_final: 0.7730 (p) REVERT: G 69 ILE cc_start: 0.7322 (tt) cc_final: 0.7071 (tt) REVERT: G 97 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.8522 (m-80) REVERT: I 32 ASP cc_start: 0.6882 (m-30) cc_final: 0.6456 (m-30) REVERT: E 183 ILE cc_start: 0.8242 (mm) cc_final: 0.7963 (mm) REVERT: E 194 LYS cc_start: 0.7772 (tmtt) cc_final: 0.7154 (tmmt) REVERT: E 1052 LEU cc_start: 0.8248 (mt) cc_final: 0.7985 (mp) REVERT: E 1163 ARG cc_start: 0.8028 (ttt90) cc_final: 0.7816 (tpt-90) REVERT: J 21 THR cc_start: 0.7937 (p) cc_final: 0.7654 (t) REVERT: J 25 SER cc_start: 0.7991 (t) cc_final: 0.7493 (p) REVERT: J 97 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8507 (m-80) REVERT: K 32 ASP cc_start: 0.7529 (m-30) cc_final: 0.7140 (m-30) outliers start: 40 outliers final: 27 residues processed: 280 average time/residue: 0.1204 time to fit residues: 51.4896 Evaluate side-chains 275 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 244 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1056 ILE Chi-restraints excluded: chain A residue 1071 THR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 1071 THR Chi-restraints excluded: chain C residue 1077 ILE Chi-restraints excluded: chain C residue 1165 GLU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 97 PHE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 1071 THR Chi-restraints excluded: chain E residue 1074 GLU Chi-restraints excluded: chain J residue 97 PHE Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 83 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 207 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 197 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 168 optimal weight: 0.0870 chunk 19 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 137 optimal weight: 10.0000 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1125 GLN ** E1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.152400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.114015 restraints weight = 20265.497| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.10 r_work: 0.3167 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17427 Z= 0.207 Angle : 0.615 12.352 23625 Z= 0.314 Chirality : 0.045 0.524 2607 Planarity : 0.004 0.044 3051 Dihedral : 5.079 50.435 2784 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.47 % Allowed : 17.71 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.17), residues: 2130 helix: 2.70 (0.27), residues: 324 sheet: 0.32 (0.22), residues: 558 loop : -1.44 (0.15), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1127 TYR 0.024 0.002 TYR E 196 PHE 0.020 0.002 PHE C 246 TRP 0.046 0.002 TRP G 47 HIS 0.005 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00495 (17382) covalent geometry : angle 0.59506 (23514) SS BOND : bond 0.00448 ( 24) SS BOND : angle 2.14571 ( 48) hydrogen bonds : bond 0.04353 ( 615) hydrogen bonds : angle 4.73150 ( 1812) link_BETA1-4 : bond 0.00282 ( 9) link_BETA1-4 : angle 1.60239 ( 27) link_NAG-ASN : bond 0.00981 ( 12) link_NAG-ASN : angle 2.95025 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 240 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ILE cc_start: 0.8692 (mm) cc_final: 0.8422 (mt) REVERT: A 211 GLN cc_start: 0.7621 (pt0) cc_final: 0.6921 (pt0) REVERT: A 264 LYS cc_start: 0.8302 (tptt) cc_final: 0.7526 (mmtm) REVERT: A 1143 LYS cc_start: 0.7447 (ttmm) cc_final: 0.7170 (ttpt) REVERT: H 21 THR cc_start: 0.8094 (p) cc_final: 0.7840 (t) REVERT: H 25 SER cc_start: 0.8305 (t) cc_final: 0.7711 (p) REVERT: L 32 ASP cc_start: 0.7099 (m-30) cc_final: 0.6834 (m-30) REVERT: L 63 SER cc_start: 0.7021 (t) cc_final: 0.6167 (p) REVERT: C 115 SER cc_start: 0.8358 (p) cc_final: 0.7937 (t) REVERT: C 194 LYS cc_start: 0.7759 (tmtt) cc_final: 0.7550 (tmmt) REVERT: C 264 LYS cc_start: 0.8284 (tptt) cc_final: 0.7633 (mmtm) REVERT: C 1024 PHE cc_start: 0.8519 (m-80) cc_final: 0.8059 (m-80) REVERT: C 1127 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7099 (ttm-80) REVERT: G 25 SER cc_start: 0.8247 (t) cc_final: 0.7792 (p) REVERT: G 69 ILE cc_start: 0.7300 (tt) cc_final: 0.7024 (tt) REVERT: I 94 TYR cc_start: 0.6460 (m-80) cc_final: 0.6256 (m-80) REVERT: E 194 LYS cc_start: 0.7834 (tmtt) cc_final: 0.7230 (tmmt) REVERT: E 1120 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7230 (mp0) REVERT: E 1163 ARG cc_start: 0.8120 (ttt90) cc_final: 0.7865 (tpt-90) REVERT: J 21 THR cc_start: 0.7969 (p) cc_final: 0.7691 (t) REVERT: J 25 SER cc_start: 0.8078 (t) cc_final: 0.7592 (p) REVERT: J 97 PHE cc_start: 0.8892 (OUTLIER) cc_final: 0.8549 (m-80) REVERT: K 32 ASP cc_start: 0.7461 (m-30) cc_final: 0.7061 (m-30) REVERT: K 94 TYR cc_start: 0.6817 (m-80) cc_final: 0.6317 (m-80) outliers start: 45 outliers final: 36 residues processed: 270 average time/residue: 0.1237 time to fit residues: 51.2899 Evaluate side-chains 273 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 235 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1056 ILE Chi-restraints excluded: chain A residue 1071 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 1071 THR Chi-restraints excluded: chain C residue 1077 ILE Chi-restraints excluded: chain C residue 1127 ARG Chi-restraints excluded: chain C residue 1165 GLU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 1067 ASP Chi-restraints excluded: chain E residue 1071 THR Chi-restraints excluded: chain E residue 1074 GLU Chi-restraints excluded: chain J residue 97 PHE Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 96 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 153 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 190 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN ** E1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1125 GLN K 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.152577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.114869 restraints weight = 20297.889| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.06 r_work: 0.3182 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17427 Z= 0.228 Angle : 0.633 12.280 23625 Z= 0.323 Chirality : 0.046 0.510 2607 Planarity : 0.004 0.048 3051 Dihedral : 5.207 51.998 2784 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.47 % Allowed : 17.98 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.17), residues: 2130 helix: 2.48 (0.27), residues: 324 sheet: 0.24 (0.22), residues: 555 loop : -1.52 (0.15), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E1124 TYR 0.024 0.002 TYR E 196 PHE 0.025 0.002 PHE C 246 TRP 0.046 0.002 TRP G 47 HIS 0.007 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00549 (17382) covalent geometry : angle 0.61424 (23514) SS BOND : bond 0.00496 ( 24) SS BOND : angle 2.13702 ( 48) hydrogen bonds : bond 0.04501 ( 615) hydrogen bonds : angle 4.83202 ( 1812) link_BETA1-4 : bond 0.00289 ( 9) link_BETA1-4 : angle 1.61246 ( 27) link_NAG-ASN : bond 0.00950 ( 12) link_NAG-ASN : angle 2.85276 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 246 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ILE cc_start: 0.8718 (mm) cc_final: 0.8435 (mt) REVERT: A 211 GLN cc_start: 0.7646 (pt0) cc_final: 0.6968 (pt0) REVERT: A 264 LYS cc_start: 0.8297 (tptt) cc_final: 0.7556 (mmtm) REVERT: A 1143 LYS cc_start: 0.7478 (ttmm) cc_final: 0.7204 (ttpt) REVERT: H 25 SER cc_start: 0.8179 (t) cc_final: 0.7627 (p) REVERT: H 39 GLN cc_start: 0.7931 (tp40) cc_final: 0.7217 (tp40) REVERT: L 32 ASP cc_start: 0.7254 (m-30) cc_final: 0.7045 (m-30) REVERT: L 63 SER cc_start: 0.7135 (t) cc_final: 0.6233 (p) REVERT: C 115 SER cc_start: 0.8373 (p) cc_final: 0.7976 (t) REVERT: C 170 LYS cc_start: 0.8245 (pttt) cc_final: 0.7808 (tppt) REVERT: C 194 LYS cc_start: 0.7788 (tmtt) cc_final: 0.7575 (tmmt) REVERT: C 205 VAL cc_start: 0.7680 (t) cc_final: 0.7450 (m) REVERT: C 264 LYS cc_start: 0.8293 (tptt) cc_final: 0.7656 (mmtm) REVERT: C 1024 PHE cc_start: 0.8496 (m-80) cc_final: 0.8056 (m-80) REVERT: C 1127 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.6973 (ttm-80) REVERT: G 25 SER cc_start: 0.8227 (t) cc_final: 0.7790 (p) REVERT: G 69 ILE cc_start: 0.7371 (tt) cc_final: 0.7107 (tt) REVERT: G 76 ASN cc_start: 0.7809 (OUTLIER) cc_final: 0.7334 (t0) REVERT: G 97 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8244 (m-80) REVERT: I 32 ASP cc_start: 0.6946 (m-30) cc_final: 0.6588 (m-30) REVERT: E 183 ILE cc_start: 0.8259 (mm) cc_final: 0.8029 (mm) REVERT: E 194 LYS cc_start: 0.7842 (tmtt) cc_final: 0.7242 (tmmt) REVERT: E 1132 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7037 (mt-10) REVERT: E 1163 ARG cc_start: 0.8172 (ttt90) cc_final: 0.7957 (tpt-90) REVERT: J 21 THR cc_start: 0.7920 (p) cc_final: 0.7645 (t) REVERT: J 25 SER cc_start: 0.8038 (t) cc_final: 0.7581 (p) REVERT: J 97 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.8467 (m-80) REVERT: K 32 ASP cc_start: 0.7483 (m-30) cc_final: 0.7080 (m-30) REVERT: K 94 TYR cc_start: 0.6882 (m-80) cc_final: 0.6311 (m-80) outliers start: 45 outliers final: 36 residues processed: 276 average time/residue: 0.1241 time to fit residues: 51.9396 Evaluate side-chains 279 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 239 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1056 ILE Chi-restraints excluded: chain A residue 1071 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 1071 THR Chi-restraints excluded: chain C residue 1077 ILE Chi-restraints excluded: chain C residue 1127 ARG Chi-restraints excluded: chain C residue 1165 GLU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain G residue 97 PHE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 1067 ASP Chi-restraints excluded: chain E residue 1071 THR Chi-restraints excluded: chain E residue 1074 GLU Chi-restraints excluded: chain E residue 1110 LEU Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 97 PHE Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 189 optimal weight: 8.9990 chunk 100 optimal weight: 0.7980 chunk 161 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 99 optimal weight: 0.2980 chunk 28 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 chunk 125 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN ** E1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.154659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.116877 restraints weight = 20252.305| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.08 r_work: 0.3175 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17427 Z= 0.132 Angle : 0.581 12.712 23625 Z= 0.294 Chirality : 0.044 0.491 2607 Planarity : 0.003 0.052 3051 Dihedral : 5.021 55.396 2784 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.97 % Allowed : 18.64 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.17), residues: 2130 helix: 2.77 (0.27), residues: 327 sheet: 0.16 (0.22), residues: 576 loop : -1.42 (0.15), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 230 TYR 0.025 0.002 TYR E 196 PHE 0.024 0.001 PHE C 246 TRP 0.040 0.001 TRP G 47 HIS 0.003 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00306 (17382) covalent geometry : angle 0.56388 (23514) SS BOND : bond 0.00350 ( 24) SS BOND : angle 1.86565 ( 48) hydrogen bonds : bond 0.04000 ( 615) hydrogen bonds : angle 4.66997 ( 1812) link_BETA1-4 : bond 0.00300 ( 9) link_BETA1-4 : angle 1.52493 ( 27) link_NAG-ASN : bond 0.00919 ( 12) link_NAG-ASN : angle 2.78251 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4345.37 seconds wall clock time: 75 minutes 3.25 seconds (4503.25 seconds total)