Starting phenix.real_space_refine on Sun Jun 15 06:08:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vee_43171/06_2025/8vee_43171.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vee_43171/06_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_43171/06_2025/8vee_43171.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vee_43171/06_2025/8vee_43171.map" model { file = "/net/cci-nas-00/data/ceres_data/8vee_43171/06_2025/8vee_43171.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vee_43171/06_2025/8vee_43171.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.78, per 1000 atoms: 0.57 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: 3.89 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 2.24 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: 5.93 Time building geometry restraints manager: 4.68 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: 0.01 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 38.420 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.100 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.600 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (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 TRP 0.044 0.002 TRP K 35 HIS 0.008 0.001 HIS A1142 PHE 0.029 0.002 PHE E1009 TYR 0.036 0.003 TYR E1094 ARG 0.015 0.001 ARG E1170 Details of bonding type rmsd link_NAG-ASN : bond 0.05741 ( 12) link_NAG-ASN : angle 4.48253 ( 36) link_BETA1-4 : bond 0.01491 ( 9) link_BETA1-4 : angle 2.44416 ( 27) hydrogen bonds : bond 0.19544 ( 615) hydrogen bonds : angle 8.56761 ( 1812) SS BOND : bond 0.01150 ( 24) SS BOND : angle 2.41924 ( 48) covalent geometry : bond 0.00632 (17382) covalent geometry : angle 1.21637 (23514) *********************** 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 : 1.764 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: 0.3074 time to fit residues: 196.9956 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 : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 122 optimal weight: 0.4980 chunk 190 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.160136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.121269 restraints weight = 20331.584| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.19 r_work: 0.3303 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17427 Z= 0.165 Angle : 0.636 13.052 23625 Z= 0.325 Chirality : 0.044 0.259 2607 Planarity : 0.005 0.057 3051 Dihedral : 6.138 59.998 2784 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.86 % Allowed : 9.05 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (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 TRP 0.013 0.001 TRP J 47 HIS 0.004 0.001 HIS A 184 PHE 0.030 0.002 PHE C1009 TYR 0.019 0.002 TYR J 35 ARG 0.006 0.001 ARG A1127 Details of bonding type rmsd link_NAG-ASN : bond 0.00589 ( 12) link_NAG-ASN : angle 1.96603 ( 36) link_BETA1-4 : bond 0.00502 ( 9) link_BETA1-4 : angle 1.88014 ( 27) hydrogen bonds : bond 0.04841 ( 615) hydrogen bonds : angle 5.78959 ( 1812) SS BOND : bond 0.00431 ( 24) SS BOND : angle 1.62461 ( 48) covalent geometry : bond 0.00382 (17382) covalent geometry : angle 0.62515 (23514) *********************** 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 333 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 299 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 GLN cc_start: 0.7320 (pt0) cc_final: 0.6682 (pt0) REVERT: A 1068 ASN cc_start: 0.8594 (t0) cc_final: 0.8337 (t0) REVERT: L 32 ASP cc_start: 0.6871 (m-30) cc_final: 0.6558 (m-30) REVERT: C 47 ASN cc_start: 0.8475 (p0) cc_final: 0.8228 (p0) REVERT: C 227 GLN cc_start: 0.7174 (OUTLIER) cc_final: 0.6783 (mt0) REVERT: C 243 THR cc_start: 0.8235 (m) cc_final: 0.8000 (m) REVERT: C 1024 PHE cc_start: 0.8064 (m-80) cc_final: 0.7814 (m-10) REVERT: G 30 SER cc_start: 0.7716 (p) cc_final: 0.7354 (t) REVERT: I 47 LEU cc_start: 0.7565 (mm) cc_final: 0.7358 (mm) REVERT: I 63 SER cc_start: 0.6109 (t) cc_final: 0.5167 (p) REVERT: E 31 GLU cc_start: 0.7487 (tt0) cc_final: 0.7161 (tt0) REVERT: E 140 ARG cc_start: 0.7105 (ttm-80) cc_final: 0.6819 (ttm-80) REVERT: E 183 ILE cc_start: 0.8283 (mm) cc_final: 0.8050 (mm) REVERT: E 211 GLN cc_start: 0.7723 (pt0) cc_final: 0.6767 (pt0) REVERT: E 212 GLN cc_start: 0.7953 (tp40) cc_final: 0.7737 (tp40) REVERT: J 100 PHE cc_start: 0.8567 (m-10) cc_final: 0.8136 (m-80) REVERT: K 32 ASP cc_start: 0.6925 (m-30) cc_final: 0.6648 (m-30) REVERT: K 47 LEU cc_start: 0.7586 (mt) cc_final: 0.7326 (mt) outliers start: 34 outliers final: 20 residues processed: 321 average time/residue: 0.2968 time to fit residues: 141.4562 Evaluate side-chains 267 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 246 time to evaluate : 1.781 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 67 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 187 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 E 18 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.150251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.111164 restraints weight = 20601.632| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.08 r_work: 0.3200 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 17427 Z= 0.334 Angle : 0.757 10.915 23625 Z= 0.391 Chirality : 0.048 0.237 2607 Planarity : 0.005 0.051 3051 Dihedral : 6.159 50.983 2784 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.67 % Allowed : 12.77 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.17), residues: 2130 helix: 1.92 (0.28), residues: 330 sheet: 0.33 (0.22), residues: 606 loop : -1.57 (0.15), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 235 HIS 0.011 0.002 HIS A 18 PHE 0.033 0.003 PHE E1009 TYR 0.031 0.003 TYR G 35 ARG 0.007 0.001 ARG C 109 Details of bonding type rmsd link_NAG-ASN : bond 0.00334 ( 12) link_NAG-ASN : angle 1.92083 ( 36) link_BETA1-4 : bond 0.00486 ( 9) link_BETA1-4 : angle 1.81816 ( 27) hydrogen bonds : bond 0.05548 ( 615) hydrogen bonds : angle 5.40114 ( 1812) SS BOND : bond 0.00653 ( 24) SS BOND : angle 2.03023 ( 48) covalent geometry : bond 0.00809 (17382) covalent geometry : angle 0.74693 (23514) *********************** 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 345 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 278 time to evaluate : 3.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ILE cc_start: 0.8672 (mm) cc_final: 0.8417 (mt) REVERT: A 211 GLN cc_start: 0.7463 (pt0) cc_final: 0.6722 (pt0) REVERT: A 1052 LEU cc_start: 0.8556 (mt) cc_final: 0.8164 (mp) REVERT: A 1066 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7289 (mt) REVERT: A 1116 ASP cc_start: 0.7889 (m-30) cc_final: 0.7666 (m-30) REVERT: A 1128 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6372 (mp0) REVERT: A 1143 LYS cc_start: 0.7126 (ttmm) cc_final: 0.6821 (ttpt) REVERT: H 21 THR cc_start: 0.8128 (p) cc_final: 0.7825 (t) REVERT: L 32 ASP cc_start: 0.7194 (m-30) cc_final: 0.6986 (m-30) REVERT: L 63 SER cc_start: 0.6369 (t) cc_final: 0.5572 (p) REVERT: C 47 ASN cc_start: 0.8780 (p0) cc_final: 0.8413 (p0) REVERT: C 194 LYS cc_start: 0.7675 (tmtt) cc_final: 0.7387 (tmmt) REVERT: C 1024 PHE cc_start: 0.8587 (m-80) cc_final: 0.8114 (m-10) REVERT: C 1143 LYS cc_start: 0.7325 (ttmm) cc_final: 0.7038 (ttpt) REVERT: G 21 THR cc_start: 0.8319 (p) cc_final: 0.7902 (t) REVERT: G 25 SER cc_start: 0.8178 (t) cc_final: 0.7713 (p) REVERT: G 69 ILE cc_start: 0.7655 (tt) cc_final: 0.7378 (tt) REVERT: G 97 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.8336 (m-80) REVERT: I 32 ASP cc_start: 0.7130 (m-30) cc_final: 0.6743 (m-30) REVERT: I 87 TYR cc_start: 0.7301 (m-80) cc_final: 0.7047 (m-80) REVERT: E 15 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8264 (mp) REVERT: E 31 GLU cc_start: 0.7489 (tt0) cc_final: 0.7273 (tt0) REVERT: E 115 SER cc_start: 0.8302 (p) cc_final: 0.8096 (t) REVERT: E 140 ARG cc_start: 0.7684 (ttm-80) cc_final: 0.7476 (ttm-80) REVERT: E 211 GLN cc_start: 0.7725 (pt0) cc_final: 0.6756 (pt0) REVERT: E 1022 TYR cc_start: 0.8939 (m-80) cc_final: 0.8716 (m-10) REVERT: J 21 THR cc_start: 0.8096 (p) cc_final: 0.7769 (t) REVERT: K 32 ASP cc_start: 0.7444 (m-30) cc_final: 0.7183 (m-30) REVERT: K 94 TYR cc_start: 0.6634 (m-80) cc_final: 0.6382 (m-80) outliers start: 67 outliers final: 43 residues processed: 329 average time/residue: 0.3251 time to fit residues: 167.5970 Evaluate side-chains 288 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 241 time to evaluate : 2.018 ------------------------------------------------------------------------------- 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 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 1059 THR Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1071 THR Chi-restraints excluded: chain A residue 1128 GLU 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 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 I residue 104 VAL Chi-restraints excluded: chain E residue 15 LEU 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 1071 THR Chi-restraints excluded: chain E residue 1117 LYS Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 72 THR 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 11 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1060 ASN ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3823 r_free = 0.3823 target = 0.158621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.120942 restraints weight = 20393.761| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.93 r_work: 0.3265 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17427 Z= 0.143 Angle : 0.613 13.133 23625 Z= 0.311 Chirality : 0.043 0.264 2607 Planarity : 0.004 0.048 3051 Dihedral : 5.532 51.832 2784 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.08 % Allowed : 15.52 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.17), residues: 2130 helix: 2.53 (0.28), residues: 324 sheet: 0.69 (0.22), residues: 558 loop : -1.47 (0.15), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 35 HIS 0.004 0.001 HIS C 17 PHE 0.020 0.002 PHE C1009 TYR 0.023 0.002 TYR E1119 ARG 0.007 0.000 ARG E 230 Details of bonding type rmsd link_NAG-ASN : bond 0.00514 ( 12) link_NAG-ASN : angle 2.45997 ( 36) link_BETA1-4 : bond 0.00395 ( 9) link_BETA1-4 : angle 1.60484 ( 27) hydrogen bonds : bond 0.04232 ( 615) hydrogen bonds : angle 4.97820 ( 1812) SS BOND : bond 0.00396 ( 24) SS BOND : angle 2.44757 ( 48) covalent geometry : bond 0.00336 (17382) covalent geometry : angle 0.59457 (23514) *********************** 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 287 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 249 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 GLN cc_start: 0.7558 (pt0) cc_final: 0.6848 (pt0) REVERT: A 264 LYS cc_start: 0.8210 (tptt) cc_final: 0.7696 (mmmt) REVERT: A 1052 LEU cc_start: 0.8399 (mt) cc_final: 0.8019 (mp) REVERT: A 1066 ILE cc_start: 0.8164 (pt) cc_final: 0.7153 (mt) REVERT: A 1128 GLU cc_start: 0.7384 (mp0) cc_final: 0.7121 (mp0) REVERT: A 1143 LYS cc_start: 0.7026 (ttmm) cc_final: 0.6776 (ttpt) REVERT: H 21 THR cc_start: 0.8046 (p) cc_final: 0.7807 (t) REVERT: L 32 ASP cc_start: 0.7201 (m-30) cc_final: 0.6915 (m-30) REVERT: L 63 SER cc_start: 0.6584 (t) cc_final: 0.5839 (p) REVERT: C 47 ASN cc_start: 0.8609 (p0) cc_final: 0.8286 (p0) REVERT: C 114 GLU cc_start: 0.7302 (pt0) cc_final: 0.7077 (pt0) REVERT: C 115 SER cc_start: 0.8487 (p) cc_final: 0.8110 (t) REVERT: C 194 LYS cc_start: 0.7737 (tmtt) cc_final: 0.7520 (tmmt) REVERT: C 264 LYS cc_start: 0.8160 (tptt) cc_final: 0.7628 (mmtm) REVERT: C 1024 PHE cc_start: 0.8383 (m-80) cc_final: 0.8108 (m-80) REVERT: G 21 THR cc_start: 0.8126 (p) cc_final: 0.7799 (t) REVERT: G 25 SER cc_start: 0.8182 (t) cc_final: 0.7777 (p) REVERT: G 69 ILE cc_start: 0.7523 (tt) cc_final: 0.7243 (tt) REVERT: G 97 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.8531 (m-80) REVERT: I 32 ASP cc_start: 0.7154 (m-30) cc_final: 0.6752 (m-30) REVERT: E 15 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8172 (mp) REVERT: E 246 PHE cc_start: 0.7784 (m-80) cc_final: 0.7549 (m-10) REVERT: E 1067 ASP cc_start: 0.7781 (t0) cc_final: 0.7392 (t0) REVERT: E 1120 GLU cc_start: 0.7347 (mt-10) cc_final: 0.7130 (mp0) REVERT: J 21 THR cc_start: 0.7970 (p) cc_final: 0.7719 (t) REVERT: K 32 ASP cc_start: 0.7519 (m-30) cc_final: 0.7217 (m-30) outliers start: 38 outliers final: 25 residues processed: 274 average time/residue: 0.3019 time to fit residues: 126.6791 Evaluate side-chains 259 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 232 time to evaluate : 1.787 ------------------------------------------------------------------------------- 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 E residue 1110 LEU Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 100 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 138 optimal weight: 7.9990 chunk 189 optimal weight: 8.9990 chunk 95 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS C1060 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.151309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.112251 restraints weight = 20634.355| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.12 r_work: 0.3160 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3834 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= 0.217 Angle : 0.648 10.263 23625 Z= 0.329 Chirality : 0.045 0.587 2607 Planarity : 0.004 0.045 3051 Dihedral : 6.098 82.232 2784 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.23 % Allowed : 15.57 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.17), residues: 2130 helix: 2.50 (0.28), residues: 324 sheet: 0.57 (0.22), residues: 555 loop : -1.50 (0.15), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 235 HIS 0.007 0.001 HIS A 18 PHE 0.022 0.002 PHE C 246 TYR 0.021 0.002 TYR J 35 ARG 0.008 0.001 ARG E1124 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 12) link_NAG-ASN : angle 2.52399 ( 36) link_BETA1-4 : bond 0.00293 ( 9) link_BETA1-4 : angle 1.66634 ( 27) hydrogen bonds : bond 0.04554 ( 615) hydrogen bonds : angle 4.95067 ( 1812) SS BOND : bond 0.00539 ( 24) SS BOND : angle 2.60421 ( 48) covalent geometry : bond 0.00522 (17382) covalent geometry : angle 0.62873 (23514) *********************** 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 303 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 244 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLN cc_start: 0.7597 (pt0) cc_final: 0.6911 (pt0) REVERT: A 264 LYS cc_start: 0.8260 (tptt) cc_final: 0.7640 (mmmt) REVERT: A 321 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8264 (ptm) REVERT: A 1052 LEU cc_start: 0.8440 (mt) cc_final: 0.8060 (mp) REVERT: A 1066 ILE cc_start: 0.8244 (pt) cc_final: 0.7254 (mt) REVERT: A 1128 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: A 1143 LYS cc_start: 0.7171 (ttmm) cc_final: 0.6934 (ttpt) REVERT: H 21 THR cc_start: 0.8105 (p) cc_final: 0.7820 (t) REVERT: H 25 SER cc_start: 0.8168 (t) cc_final: 0.7579 (p) REVERT: L 32 ASP cc_start: 0.7171 (m-30) cc_final: 0.6957 (m-30) REVERT: L 63 SER cc_start: 0.6588 (t) cc_final: 0.5820 (p) REVERT: C 47 ASN cc_start: 0.8679 (p0) cc_final: 0.8256 (p0) REVERT: C 70 ILE cc_start: 0.8652 (mm) cc_final: 0.8344 (mt) REVERT: C 114 GLU cc_start: 0.7351 (pt0) cc_final: 0.7101 (pt0) REVERT: C 115 SER cc_start: 0.8553 (p) cc_final: 0.8015 (t) REVERT: C 194 LYS cc_start: 0.7736 (tmtt) cc_final: 0.7476 (tmmt) REVERT: C 264 LYS cc_start: 0.8260 (tptt) cc_final: 0.7621 (mmtm) REVERT: C 1024 PHE cc_start: 0.8525 (m-80) cc_final: 0.8059 (m-80) REVERT: G 21 THR cc_start: 0.8124 (p) cc_final: 0.7746 (t) REVERT: G 25 SER cc_start: 0.8173 (t) cc_final: 0.7737 (p) REVERT: G 69 ILE cc_start: 0.7562 (tt) cc_final: 0.7307 (tt) REVERT: G 97 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8390 (m-80) REVERT: I 32 ASP cc_start: 0.7127 (m-30) cc_final: 0.6681 (m-30) REVERT: E 1067 ASP cc_start: 0.7928 (t0) cc_final: 0.7474 (t0) REVERT: E 1120 GLU cc_start: 0.7327 (mt-10) cc_final: 0.6979 (mp0) REVERT: E 1128 GLU cc_start: 0.7304 (mm-30) cc_final: 0.7094 (mm-30) REVERT: J 21 THR cc_start: 0.7997 (p) cc_final: 0.7673 (t) REVERT: K 4 MET cc_start: 0.7910 (mmp) cc_final: 0.7681 (mmp) REVERT: K 32 ASP cc_start: 0.7471 (m-30) cc_final: 0.7150 (m-30) REVERT: K 90 GLN cc_start: 0.7966 (pp30) cc_final: 0.7657 (pp30) outliers start: 59 outliers final: 43 residues processed: 285 average time/residue: 0.3351 time to fit residues: 147.9442 Evaluate side-chains 282 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 236 time to evaluate : 1.888 ------------------------------------------------------------------------------- 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 198 SER 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 1071 THR Chi-restraints excluded: chain A residue 1128 GLU Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain L residue 47 LEU 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 1077 ILE Chi-restraints excluded: chain C residue 1110 LEU 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 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 222 THR 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 E residue 1102 MET 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 100 VAL Chi-restraints excluded: chain K residue 52 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 54 optimal weight: 0.5980 chunk 113 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 182 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 17 HIS E 156 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.153555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.114994 restraints weight = 20367.974| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.11 r_work: 0.3196 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17427 Z= 0.142 Angle : 0.578 13.842 23625 Z= 0.293 Chirality : 0.043 0.581 2607 Planarity : 0.003 0.044 3051 Dihedral : 5.310 59.438 2784 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.58 % Allowed : 17.05 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.17), residues: 2130 helix: 2.76 (0.28), residues: 324 sheet: 0.42 (0.22), residues: 573 loop : -1.38 (0.15), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 47 HIS 0.004 0.001 HIS A 18 PHE 0.019 0.002 PHE A 246 TYR 0.018 0.001 TYR J 50 ARG 0.008 0.000 ARG E 230 Details of bonding type rmsd link_NAG-ASN : bond 0.00930 ( 12) link_NAG-ASN : angle 3.19060 ( 36) link_BETA1-4 : bond 0.00368 ( 9) link_BETA1-4 : angle 1.60196 ( 27) hydrogen bonds : bond 0.04029 ( 615) hydrogen bonds : angle 4.73271 ( 1812) SS BOND : bond 0.00400 ( 24) SS BOND : angle 2.05725 ( 48) covalent geometry : bond 0.00331 (17382) covalent geometry : angle 0.55560 (23514) *********************** 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 304 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 257 time to evaluate : 3.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLN cc_start: 0.7891 (pt0) cc_final: 0.7186 (pt0) REVERT: A 264 LYS cc_start: 0.8202 (tptt) cc_final: 0.7472 (mmtm) REVERT: A 1052 LEU cc_start: 0.8412 (mt) cc_final: 0.8017 (mp) REVERT: A 1143 LYS cc_start: 0.7234 (ttmm) cc_final: 0.6911 (ttpt) REVERT: H 21 THR cc_start: 0.8074 (p) cc_final: 0.7818 (t) REVERT: H 25 SER cc_start: 0.8016 (t) cc_final: 0.7454 (p) REVERT: L 32 ASP cc_start: 0.7241 (m-30) cc_final: 0.7009 (m-30) REVERT: L 63 SER cc_start: 0.6649 (t) cc_final: 0.5892 (p) REVERT: C 47 ASN cc_start: 0.8666 (p0) cc_final: 0.8169 (p0) REVERT: C 115 SER cc_start: 0.8411 (p) cc_final: 0.7913 (t) REVERT: C 194 LYS cc_start: 0.7706 (tmtt) cc_final: 0.7473 (tmmt) REVERT: C 264 LYS cc_start: 0.8193 (tptt) cc_final: 0.7560 (mmtm) REVERT: C 1024 PHE cc_start: 0.8492 (m-80) cc_final: 0.8011 (m-10) REVERT: G 21 THR cc_start: 0.8097 (p) cc_final: 0.7736 (t) REVERT: G 25 SER cc_start: 0.8248 (t) cc_final: 0.7792 (p) REVERT: G 69 ILE cc_start: 0.7526 (tt) cc_final: 0.7269 (tt) REVERT: G 97 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8503 (m-80) REVERT: I 4 MET cc_start: 0.7687 (tpp) cc_final: 0.7154 (tpp) REVERT: I 32 ASP cc_start: 0.7142 (m-30) cc_final: 0.6928 (m-30) REVERT: E 194 LYS cc_start: 0.7761 (tmtt) cc_final: 0.7202 (tmmt) REVERT: E 1067 ASP cc_start: 0.7877 (t0) cc_final: 0.7434 (t0) REVERT: E 1120 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6897 (mp0) REVERT: E 1143 LYS cc_start: 0.7644 (ttmm) cc_final: 0.7435 (ttpt) REVERT: E 1163 ARG cc_start: 0.8079 (ttt90) cc_final: 0.7806 (tpt-90) REVERT: J 21 THR cc_start: 0.7985 (p) cc_final: 0.7676 (t) REVERT: K 32 ASP cc_start: 0.7496 (m-30) cc_final: 0.7128 (m-30) REVERT: K 90 GLN cc_start: 0.7981 (pp30) cc_final: 0.7658 (pp30) REVERT: K 95 GLN cc_start: 0.7154 (mp10) cc_final: 0.6871 (mp10) outliers start: 47 outliers final: 36 residues processed: 286 average time/residue: 0.4402 time to fit residues: 196.8410 Evaluate side-chains 287 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 250 time to evaluate : 2.053 ------------------------------------------------------------------------------- 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 238 LEU Chi-restraints excluded: chain A residue 273 GLN 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 70 SER 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 136 THR Chi-restraints excluded: chain C residue 178 LEU 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 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 G residue 100 VAL Chi-restraints excluded: chain E residue 75 GLN 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 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 E residue 1110 LEU Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 70 SER 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 128 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 58 optimal weight: 0.0770 chunk 69 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1159 HIS ** K 6 GLN ** 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 = 0.3762 r_free = 0.3762 target = 0.154189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.115798 restraints weight = 20302.056| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.10 r_work: 0.3205 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17427 Z= 0.127 Angle : 0.565 13.467 23625 Z= 0.287 Chirality : 0.043 0.579 2607 Planarity : 0.003 0.041 3051 Dihedral : 5.068 53.109 2784 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.36 % Allowed : 17.38 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.17), residues: 2130 helix: 2.87 (0.28), residues: 324 sheet: 0.40 (0.22), residues: 573 loop : -1.33 (0.15), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 47 HIS 0.003 0.001 HIS C 17 PHE 0.017 0.001 PHE C 246 TYR 0.025 0.001 TYR E 196 ARG 0.010 0.000 ARG E1124 Details of bonding type rmsd link_NAG-ASN : bond 0.01084 ( 12) link_NAG-ASN : angle 3.11343 ( 36) link_BETA1-4 : bond 0.00342 ( 9) link_BETA1-4 : angle 1.57379 ( 27) hydrogen bonds : bond 0.03900 ( 615) hydrogen bonds : angle 4.60484 ( 1812) SS BOND : bond 0.00365 ( 24) SS BOND : angle 1.89840 ( 48) covalent geometry : bond 0.00296 (17382) covalent geometry : angle 0.54398 (23514) *********************** 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 294 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 251 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7449 (mm-30) REVERT: A 211 GLN cc_start: 0.7868 (pt0) cc_final: 0.7115 (pt0) REVERT: A 257 ARG cc_start: 0.8397 (mtm-85) cc_final: 0.8163 (mtm180) REVERT: A 264 LYS cc_start: 0.8195 (tptt) cc_final: 0.7439 (mmtm) REVERT: A 1066 ILE cc_start: 0.8189 (pt) cc_final: 0.7233 (mt) REVERT: A 1143 LYS cc_start: 0.7363 (ttmm) cc_final: 0.6994 (ttpt) REVERT: A 1163 ARG cc_start: 0.8221 (ttt90) cc_final: 0.7565 (tpt-90) REVERT: H 21 THR cc_start: 0.8102 (p) cc_final: 0.7841 (t) REVERT: H 25 SER cc_start: 0.8312 (t) cc_final: 0.7693 (p) REVERT: L 32 ASP cc_start: 0.7205 (m-30) cc_final: 0.6964 (m-30) REVERT: L 63 SER cc_start: 0.6641 (t) cc_final: 0.5908 (p) REVERT: C 47 ASN cc_start: 0.8669 (p0) cc_final: 0.8087 (p0) REVERT: C 115 SER cc_start: 0.8366 (p) cc_final: 0.7935 (t) REVERT: C 194 LYS cc_start: 0.7699 (tmtt) cc_final: 0.7480 (tmmt) REVERT: C 264 LYS cc_start: 0.8211 (tptt) cc_final: 0.7568 (mmtm) REVERT: C 1024 PHE cc_start: 0.8517 (m-80) cc_final: 0.7951 (m-10) REVERT: G 25 SER cc_start: 0.8261 (t) cc_final: 0.7823 (p) REVERT: G 69 ILE cc_start: 0.7411 (tt) cc_final: 0.7163 (tt) REVERT: G 97 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.8443 (m-80) REVERT: I 32 ASP cc_start: 0.7136 (m-30) cc_final: 0.6912 (m-30) REVERT: E 183 ILE cc_start: 0.8246 (mm) cc_final: 0.7971 (mm) REVERT: E 194 LYS cc_start: 0.7780 (tmtt) cc_final: 0.7174 (tmmt) REVERT: E 1067 ASP cc_start: 0.7892 (t0) cc_final: 0.7451 (t0) REVERT: E 1120 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6954 (mm-30) REVERT: E 1163 ARG cc_start: 0.8061 (ttt90) cc_final: 0.7807 (tpt-90) REVERT: J 21 THR cc_start: 0.7979 (p) cc_final: 0.7686 (t) REVERT: K 32 ASP cc_start: 0.7494 (m-30) cc_final: 0.7130 (m-30) outliers start: 43 outliers final: 34 residues processed: 282 average time/residue: 0.2927 time to fit residues: 126.0663 Evaluate side-chains 274 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 239 time to evaluate : 1.722 ------------------------------------------------------------------------------- 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 198 SER Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 1071 THR 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 56 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 37 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 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 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 G residue 100 VAL Chi-restraints excluded: chain E residue 75 GLN 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 K residue 63 SER 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 48 optimal weight: 0.2980 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 187 optimal weight: 0.3980 chunk 59 optimal weight: 0.8980 chunk 118 optimal weight: 10.0000 chunk 115 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 170 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** E1125 GLN ** K 6 GLN ** 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 = 0.3771 r_free = 0.3771 target = 0.154869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.116833 restraints weight = 20255.638| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.07 r_work: 0.3251 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17427 Z= 0.127 Angle : 0.555 13.292 23625 Z= 0.283 Chirality : 0.043 0.549 2607 Planarity : 0.003 0.044 3051 Dihedral : 4.897 54.184 2784 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.58 % Allowed : 17.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.17), residues: 2130 helix: 2.95 (0.28), residues: 324 sheet: 0.40 (0.22), residues: 573 loop : -1.31 (0.15), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 47 HIS 0.003 0.001 HIS C 17 PHE 0.022 0.001 PHE C 246 TYR 0.018 0.001 TYR J 50 ARG 0.008 0.000 ARG E 230 Details of bonding type rmsd link_NAG-ASN : bond 0.00979 ( 12) link_NAG-ASN : angle 2.99251 ( 36) link_BETA1-4 : bond 0.00359 ( 9) link_BETA1-4 : angle 1.54712 ( 27) hydrogen bonds : bond 0.03866 ( 615) hydrogen bonds : angle 4.55737 ( 1812) SS BOND : bond 0.00327 ( 24) SS BOND : angle 1.70788 ( 48) covalent geometry : bond 0.00297 (17382) covalent geometry : angle 0.53575 (23514) *********************** 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 292 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 245 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7445 (mm-30) REVERT: A 211 GLN cc_start: 0.7879 (pt0) cc_final: 0.7143 (pt0) REVERT: A 257 ARG cc_start: 0.8405 (mtm-85) cc_final: 0.8176 (mtm180) REVERT: A 264 LYS cc_start: 0.8184 (tptt) cc_final: 0.7394 (mmtm) REVERT: A 1066 ILE cc_start: 0.8199 (pt) cc_final: 0.7251 (mt) REVERT: A 1143 LYS cc_start: 0.7417 (ttmm) cc_final: 0.7113 (ttpt) REVERT: A 1163 ARG cc_start: 0.8230 (ttt90) cc_final: 0.7474 (tpt-90) REVERT: H 21 THR cc_start: 0.8097 (p) cc_final: 0.7850 (t) REVERT: H 25 SER cc_start: 0.8258 (t) cc_final: 0.7654 (p) REVERT: L 32 ASP cc_start: 0.7254 (m-30) cc_final: 0.7007 (m-30) REVERT: L 63 SER cc_start: 0.6738 (t) cc_final: 0.6089 (p) REVERT: C 47 ASN cc_start: 0.8740 (p0) cc_final: 0.8216 (p0) REVERT: C 114 GLU cc_start: 0.6862 (pt0) cc_final: 0.6581 (pt0) REVERT: C 115 SER cc_start: 0.8326 (p) cc_final: 0.7900 (t) REVERT: C 194 LYS cc_start: 0.7716 (tmtt) cc_final: 0.7504 (tmmt) REVERT: C 264 LYS cc_start: 0.8187 (tptt) cc_final: 0.7573 (mmtm) REVERT: C 1024 PHE cc_start: 0.8476 (m-80) cc_final: 0.7977 (m-10) REVERT: C 1103 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7362 (mt-10) REVERT: G 25 SER cc_start: 0.8178 (t) cc_final: 0.7740 (p) REVERT: G 69 ILE cc_start: 0.7233 (tt) cc_final: 0.6968 (tt) REVERT: G 97 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8451 (m-80) REVERT: I 4 MET cc_start: 0.7814 (tpp) cc_final: 0.7302 (tpp) REVERT: I 32 ASP cc_start: 0.7141 (m-30) cc_final: 0.6909 (m-30) REVERT: E 183 ILE cc_start: 0.8282 (mm) cc_final: 0.7980 (mm) REVERT: E 1067 ASP cc_start: 0.7919 (t0) cc_final: 0.7490 (t0) REVERT: E 1163 ARG cc_start: 0.8061 (ttt90) cc_final: 0.7818 (tpt-90) REVERT: J 21 THR cc_start: 0.7967 (p) cc_final: 0.7694 (t) REVERT: J 25 SER cc_start: 0.7987 (t) cc_final: 0.7482 (p) REVERT: K 32 ASP cc_start: 0.7536 (m-30) cc_final: 0.7157 (m-30) outliers start: 47 outliers final: 38 residues processed: 282 average time/residue: 0.2942 time to fit residues: 125.0714 Evaluate side-chains 279 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 240 time to evaluate : 1.844 ------------------------------------------------------------------------------- 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 198 SER Chi-restraints excluded: chain A residue 273 GLN 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 58 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 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 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 1010 ILE 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 G residue 100 VAL 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 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 100 VAL 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 56 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 chunk 113 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 9 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1159 HIS G 76 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.154965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.116894 restraints weight = 20432.143| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.09 r_work: 0.3254 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17427 Z= 0.124 Angle : 0.551 12.561 23625 Z= 0.281 Chirality : 0.043 0.501 2607 Planarity : 0.003 0.043 3051 Dihedral : 4.809 54.634 2784 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.41 % Allowed : 17.38 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.18), residues: 2130 helix: 3.02 (0.27), residues: 327 sheet: 0.31 (0.22), residues: 591 loop : -1.23 (0.16), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP G 47 HIS 0.003 0.001 HIS C 17 PHE 0.020 0.001 PHE C 246 TYR 0.020 0.001 TYR G 50 ARG 0.011 0.000 ARG E1124 Details of bonding type rmsd link_NAG-ASN : bond 0.00929 ( 12) link_NAG-ASN : angle 2.84260 ( 36) link_BETA1-4 : bond 0.00363 ( 9) link_BETA1-4 : angle 1.51076 ( 27) hydrogen bonds : bond 0.03815 ( 615) hydrogen bonds : angle 4.51425 ( 1812) SS BOND : bond 0.00340 ( 24) SS BOND : angle 1.70689 ( 48) covalent geometry : bond 0.00289 (17382) covalent geometry : angle 0.53292 (23514) *********************** 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 290 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 246 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7436 (mm-30) REVERT: A 211 GLN cc_start: 0.7897 (pt0) cc_final: 0.7150 (pt0) REVERT: A 257 ARG cc_start: 0.8383 (mtm-85) cc_final: 0.8161 (mtm180) REVERT: A 264 LYS cc_start: 0.8187 (tptt) cc_final: 0.7407 (mmtm) REVERT: A 278 CYS cc_start: 0.5895 (OUTLIER) cc_final: 0.5560 (p) REVERT: A 1066 ILE cc_start: 0.8175 (pt) cc_final: 0.7226 (mt) REVERT: A 1143 LYS cc_start: 0.7459 (ttmm) cc_final: 0.7152 (ttpt) REVERT: A 1163 ARG cc_start: 0.8275 (ttt90) cc_final: 0.7444 (tpt-90) REVERT: H 21 THR cc_start: 0.8098 (p) cc_final: 0.7847 (t) REVERT: H 25 SER cc_start: 0.8258 (t) cc_final: 0.7656 (p) REVERT: L 32 ASP cc_start: 0.7221 (m-30) cc_final: 0.6973 (m-30) REVERT: L 63 SER cc_start: 0.6788 (t) cc_final: 0.6145 (p) REVERT: C 47 ASN cc_start: 0.8731 (p0) cc_final: 0.8228 (p0) REVERT: C 114 GLU cc_start: 0.6832 (pt0) cc_final: 0.6579 (mt-10) REVERT: C 115 SER cc_start: 0.8301 (p) cc_final: 0.7859 (t) REVERT: C 194 LYS cc_start: 0.7675 (tmtt) cc_final: 0.7460 (tmmt) REVERT: C 264 LYS cc_start: 0.8163 (tptt) cc_final: 0.7570 (mmtm) REVERT: C 1024 PHE cc_start: 0.8478 (m-80) cc_final: 0.7973 (m-10) REVERT: G 25 SER cc_start: 0.8119 (t) cc_final: 0.7670 (p) REVERT: G 69 ILE cc_start: 0.7189 (tt) cc_final: 0.6931 (tt) REVERT: G 76 ASN cc_start: 0.7560 (OUTLIER) cc_final: 0.7031 (t0) REVERT: G 97 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.8445 (m-80) REVERT: I 32 ASP cc_start: 0.7187 (m-30) cc_final: 0.6949 (m-30) REVERT: E 183 ILE cc_start: 0.8307 (mm) cc_final: 0.7986 (mm) REVERT: E 1052 LEU cc_start: 0.8309 (mt) cc_final: 0.8027 (mp) REVERT: E 1067 ASP cc_start: 0.7941 (t0) cc_final: 0.7497 (t0) REVERT: E 1120 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6876 (mp0) REVERT: E 1163 ARG cc_start: 0.8028 (ttt90) cc_final: 0.7793 (tpt-90) REVERT: J 21 THR cc_start: 0.7973 (p) cc_final: 0.7701 (t) REVERT: J 25 SER cc_start: 0.7991 (t) cc_final: 0.7495 (p) REVERT: K 32 ASP cc_start: 0.7546 (m-30) cc_final: 0.7165 (m-30) outliers start: 44 outliers final: 36 residues processed: 281 average time/residue: 0.2930 time to fit residues: 124.9152 Evaluate side-chains 281 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 242 time to evaluate : 1.698 ------------------------------------------------------------------------------- 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 198 SER 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 58 SER Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain L residue 56 SER 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 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 1010 ILE Chi-restraints excluded: chain C residue 1067 ASP 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 76 ASN 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 E residue 75 GLN 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 324 VAL Chi-restraints excluded: chain E residue 1071 THR Chi-restraints excluded: chain E residue 1074 GLU Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 63 SER 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 108 optimal weight: 3.9990 chunk 118 optimal weight: 0.0770 chunk 188 optimal weight: 0.5980 chunk 156 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 101 optimal weight: 0.0980 chunk 61 optimal weight: 20.0000 chunk 141 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 171 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 overall best weight: 0.5140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.154267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.115997 restraints weight = 20341.795| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.08 r_work: 0.3254 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 17427 Z= 0.161 Angle : 0.739 59.175 23625 Z= 0.417 Chirality : 0.044 0.508 2607 Planarity : 0.003 0.043 3051 Dihedral : 4.802 54.654 2784 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.30 % Allowed : 17.49 % Favored : 80.21 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.18), residues: 2130 helix: 3.04 (0.27), residues: 327 sheet: 0.31 (0.22), residues: 591 loop : -1.22 (0.16), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP G 47 HIS 0.003 0.001 HIS A 18 PHE 0.018 0.001 PHE C 246 TYR 0.019 0.001 TYR G 50 ARG 0.010 0.000 ARG E1124 Details of bonding type rmsd link_NAG-ASN : bond 0.00949 ( 12) link_NAG-ASN : angle 2.93006 ( 36) link_BETA1-4 : bond 0.00323 ( 9) link_BETA1-4 : angle 1.50478 ( 27) hydrogen bonds : bond 0.03838 ( 615) hydrogen bonds : angle 4.51364 ( 1812) SS BOND : bond 0.00319 ( 24) SS BOND : angle 1.68067 ( 48) covalent geometry : bond 0.00349 (17382) covalent geometry : angle 0.72603 (23514) ********************** 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 284 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 242 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7433 (mm-30) REVERT: A 211 GLN cc_start: 0.7898 (pt0) cc_final: 0.7153 (pt0) REVERT: A 257 ARG cc_start: 0.8377 (mtm-85) cc_final: 0.8152 (mtm180) REVERT: A 264 LYS cc_start: 0.8178 (tptt) cc_final: 0.7403 (mmtm) REVERT: A 278 CYS cc_start: 0.5874 (OUTLIER) cc_final: 0.5545 (p) REVERT: A 1066 ILE cc_start: 0.8179 (pt) cc_final: 0.7227 (mt) REVERT: A 1143 LYS cc_start: 0.7455 (ttmm) cc_final: 0.7149 (ttpt) REVERT: A 1163 ARG cc_start: 0.8232 (ttt90) cc_final: 0.7447 (tpt-90) REVERT: H 21 THR cc_start: 0.8102 (p) cc_final: 0.7852 (t) REVERT: H 25 SER cc_start: 0.8264 (t) cc_final: 0.7661 (p) REVERT: L 32 ASP cc_start: 0.7216 (m-30) cc_final: 0.6973 (m-30) REVERT: L 63 SER cc_start: 0.6781 (t) cc_final: 0.6141 (p) REVERT: C 47 ASN cc_start: 0.8716 (p0) cc_final: 0.8226 (p0) REVERT: C 114 GLU cc_start: 0.6824 (pt0) cc_final: 0.6566 (mt-10) REVERT: C 115 SER cc_start: 0.8285 (p) cc_final: 0.7855 (t) REVERT: C 194 LYS cc_start: 0.7674 (tmtt) cc_final: 0.7463 (tmmt) REVERT: C 264 LYS cc_start: 0.8169 (tptt) cc_final: 0.7569 (mmtm) REVERT: C 1024 PHE cc_start: 0.8475 (m-80) cc_final: 0.7971 (m-10) REVERT: G 25 SER cc_start: 0.8108 (t) cc_final: 0.7663 (p) REVERT: G 69 ILE cc_start: 0.7187 (tt) cc_final: 0.6927 (tt) REVERT: G 97 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8448 (m-80) REVERT: I 32 ASP cc_start: 0.7188 (m-30) cc_final: 0.6948 (m-30) REVERT: E 183 ILE cc_start: 0.8310 (mm) cc_final: 0.7995 (mm) REVERT: E 1052 LEU cc_start: 0.8312 (mt) cc_final: 0.8029 (mp) REVERT: E 1067 ASP cc_start: 0.7950 (t0) cc_final: 0.7503 (t0) REVERT: E 1120 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6902 (mp0) REVERT: E 1163 ARG cc_start: 0.8025 (ttt90) cc_final: 0.7794 (tpt-90) REVERT: J 21 THR cc_start: 0.7973 (p) cc_final: 0.7704 (t) REVERT: J 25 SER cc_start: 0.7985 (t) cc_final: 0.7490 (p) REVERT: K 32 ASP cc_start: 0.7550 (m-30) cc_final: 0.7168 (m-30) outliers start: 42 outliers final: 39 residues processed: 275 average time/residue: 0.2986 time to fit residues: 125.5090 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 : 1.921 ------------------------------------------------------------------------------- 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 198 SER 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 58 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 35 GLU 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 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 1010 ILE Chi-restraints excluded: chain C residue 1067 ASP 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 G residue 100 VAL Chi-restraints excluded: chain E residue 75 GLN 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 324 VAL Chi-restraints excluded: chain E residue 1071 THR Chi-restraints excluded: chain E residue 1074 GLU Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 63 SER 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 137 optimal weight: 10.0000 chunk 71 optimal weight: 0.4980 chunk 50 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 190 optimal weight: 8.9990 chunk 130 optimal weight: 20.0000 chunk 9 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 141 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.154204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.115938 restraints weight = 20364.309| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.08 r_work: 0.3252 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 17427 Z= 0.161 Angle : 0.739 59.175 23625 Z= 0.417 Chirality : 0.044 0.508 2607 Planarity : 0.003 0.043 3051 Dihedral : 4.802 54.654 2784 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.25 % Allowed : 17.65 % Favored : 80.10 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.18), residues: 2130 helix: 3.04 (0.27), residues: 327 sheet: 0.31 (0.22), residues: 591 loop : -1.22 (0.16), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP G 47 HIS 0.003 0.001 HIS A 18 PHE 0.018 0.001 PHE C 246 TYR 0.019 0.001 TYR G 50 ARG 0.010 0.000 ARG E1124 Details of bonding type rmsd link_NAG-ASN : bond 0.00949 ( 12) link_NAG-ASN : angle 2.93006 ( 36) link_BETA1-4 : bond 0.00323 ( 9) link_BETA1-4 : angle 1.50478 ( 27) hydrogen bonds : bond 0.03838 ( 615) hydrogen bonds : angle 4.51364 ( 1812) SS BOND : bond 0.00319 ( 24) SS BOND : angle 1.68067 ( 48) covalent geometry : bond 0.00349 (17382) covalent geometry : angle 0.72603 (23514) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10345.98 seconds wall clock time: 182 minutes 24.41 seconds (10944.41 seconds total)