Starting phenix.real_space_refine on Thu Sep 26 08:32:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7h_27230/09_2024/8d7h_27230.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7h_27230/09_2024/8d7h_27230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7h_27230/09_2024/8d7h_27230.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7h_27230/09_2024/8d7h_27230.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7h_27230/09_2024/8d7h_27230.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7h_27230/09_2024/8d7h_27230.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 7970 2.51 5 N 2156 2.21 5 O 2368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 125 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12540 Number of models: 1 Model: "" Number of chains: 22 Chain: "C" Number of atoms: 2259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2259 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 24, 'TRANS': 257} Chain: "D" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1432 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 16, 'TRANS': 161} Chain: "A" Number of atoms: 2355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2355 Classifications: {'peptide': 303} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 280} Chain: "G" Number of atoms: 2259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2259 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 24, 'TRANS': 257} Chain: "H" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1432 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 16, 'TRANS': 161} Chain: "E" Number of atoms: 2355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2355 Classifications: {'peptide': 303} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 280} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.49, per 1000 atoms: 0.68 Number of scatterers: 12540 At special positions: 0 Unit cell: (196.94, 156.52, 101.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 2368 8.00 N 2156 7.00 C 7970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 127 " distance=2.04 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 143 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 116 " - pdb=" SG CYS G 127 " distance=2.04 Simple disulfide: pdb=" SG CYS G 154 " - pdb=" SG CYS G 164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 116 " distance=2.03 Simple disulfide: pdb=" SG CYS E 143 " - pdb=" SG CYS E 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 184 " - pdb=" SG CYS E 195 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG F 1 " - " NAG F 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 501 " - " ASN A 168 " " NAG A 502 " - " ASN A 292 " " NAG B 1 " - " ASN C 190 " " NAG E 501 " - " ASN E 168 " " NAG E 502 " - " ASN E 292 " " NAG F 1 " - " ASN C 70 " " NAG I 1 " - " ASN C 60 " " NAG J 1 " - " ASN C 142 " " NAG K 1 " - " ASN A 92 " " NAG L 1 " - " ASN A 104 " " NAG M 1 " - " ASN A 140 " " NAG N 1 " - " ASN G 190 " " NAG O 1 " - " ASN G 70 " " NAG P 1 " - " ASN G 60 " " NAG Q 1 " - " ASN G 142 " " NAG R 1 " - " ASN E 92 " " NAG S 1 " - " ASN E 104 " " NAG T 1 " - " ASN E 140 " Time building additional restraints: 3.28 Conformation dependent library (CDL) restraints added in 1.5 seconds 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2860 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 26 sheets defined 19.5% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.560A pdb=" N HIS C 83 " --> pdb=" O GLU C 80 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER C 84 " --> pdb=" O LEU C 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 80 through 84' Processing helix chain 'D' and resid 35 through 66 removed outlier: 4.252A pdb=" N SER D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE D 40 " --> pdb=" O PRO D 36 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 90 through 97 removed outlier: 3.625A pdb=" N LEU D 97 " --> pdb=" O VAL D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 120 Processing helix chain 'D' and resid 121 through 123 No H-bonds generated for 'chain 'D' and resid 121 through 123' Processing helix chain 'D' and resid 126 through 154 Processing helix chain 'D' and resid 176 through 208 Processing helix chain 'A' and resid 69 through 74 removed outlier: 3.819A pdb=" N LEU A 74 " --> pdb=" O THR A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 Processing helix chain 'G' and resid 65 through 67 No H-bonds generated for 'chain 'G' and resid 65 through 67' Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.526A pdb=" N HIS G 83 " --> pdb=" O GLU G 80 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER G 84 " --> pdb=" O LEU G 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 80 through 84' Processing helix chain 'H' and resid 35 through 66 removed outlier: 4.251A pdb=" N SER H 39 " --> pdb=" O GLY H 35 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE H 40 " --> pdb=" O PRO H 36 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN H 41 " --> pdb=" O GLY H 37 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY H 66 " --> pdb=" O LEU H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 71 Processing helix chain 'H' and resid 90 through 97 removed outlier: 3.637A pdb=" N LEU H 97 " --> pdb=" O VAL H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 120 Processing helix chain 'H' and resid 121 through 123 No H-bonds generated for 'chain 'H' and resid 121 through 123' Processing helix chain 'H' and resid 126 through 154 Processing helix chain 'H' and resid 176 through 208 Processing helix chain 'E' and resid 69 through 74 removed outlier: 3.948A pdb=" N LEU E 74 " --> pdb=" O THR E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 231 Processing sheet with id=AA1, first strand: chain 'C' and resid 32 through 36 removed outlier: 6.379A pdb=" N HIS C 32 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N HIS C 104 " --> pdb=" O HIS C 32 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLN C 34 " --> pdb=" O HIS C 104 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU C 97 " --> pdb=" O HIS C 91 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N HIS C 91 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N HIS C 99 " --> pdb=" O CYS C 89 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS C 89 " --> pdb=" O HIS C 99 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 101 " --> pdb=" O TYR C 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 41 through 45 removed outlier: 3.602A pdb=" N VAL C 42 " --> pdb=" O LEU C 76 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 113 through 114 removed outlier: 3.758A pdb=" N HIS C 130 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 140 through 145 removed outlier: 3.684A pdb=" N THR C 144 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN C 190 " --> pdb=" O VAL C 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 211 through 214 removed outlier: 3.657A pdb=" N VAL C 224 " --> pdb=" O HIS C 265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 255 through 258 removed outlier: 3.544A pdb=" N GLN C 255 " --> pdb=" O TYR C 246 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR C 246 " --> pdb=" O GLN C 255 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE C 243 " --> pdb=" O ALA C 281 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 42 through 44 removed outlier: 3.589A pdb=" N VAL A 42 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A 61 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 91 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 49 through 51 removed outlier: 3.665A pdb=" N GLY A 132 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A 125 " --> pdb=" O CYS A 116 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 186 through 187 removed outlier: 4.008A pdb=" N GLU A 186 " --> pdb=" O HIS A 196 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR A 156 " --> pdb=" O ASN A 140 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ASN A 140 " --> pdb=" O THR A 156 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N THR A 234 " --> pdb=" O CYS A 143 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N SER A 145 " --> pdb=" O THR A 234 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 182 through 183 Processing sheet with id=AB2, first strand: chain 'A' and resid 182 through 183 Processing sheet with id=AB3, first strand: chain 'A' and resid 242 through 244 Processing sheet with id=AB4, first strand: chain 'A' and resid 284 through 286 removed outlier: 3.540A pdb=" N PHE A 308 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 32 through 36 removed outlier: 6.402A pdb=" N HIS G 32 " --> pdb=" O LEU G 102 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N HIS G 104 " --> pdb=" O HIS G 32 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLN G 34 " --> pdb=" O HIS G 104 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LEU G 97 " --> pdb=" O HIS G 91 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N HIS G 91 " --> pdb=" O LEU G 97 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS G 99 " --> pdb=" O CYS G 89 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 41 through 45 removed outlier: 3.508A pdb=" N VAL G 42 " --> pdb=" O LEU G 76 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 113 through 114 removed outlier: 3.756A pdb=" N HIS G 130 " --> pdb=" O VAL G 113 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 140 through 145 removed outlier: 3.685A pdb=" N THR G 144 " --> pdb=" O SER G 180 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN G 190 " --> pdb=" O VAL G 183 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 211 through 214 removed outlier: 3.731A pdb=" N VAL G 224 " --> pdb=" O HIS G 265 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 255 through 258 removed outlier: 3.689A pdb=" N GLN G 255 " --> pdb=" O TYR G 246 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR G 246 " --> pdb=" O GLN G 255 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL G 257 " --> pdb=" O LEU G 244 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE G 243 " --> pdb=" O ALA G 281 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 42 through 44 removed outlier: 3.572A pdb=" N VAL E 42 " --> pdb=" O SER E 61 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER E 61 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N THR E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU E 91 " --> pdb=" O THR E 95 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 49 through 51 removed outlier: 3.665A pdb=" N GLY E 132 " --> pdb=" O LEU E 50 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA E 125 " --> pdb=" O CYS E 116 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 186 through 187 removed outlier: 4.002A pdb=" N GLU E 186 " --> pdb=" O HIS E 196 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR E 156 " --> pdb=" O ASN E 140 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ASN E 140 " --> pdb=" O THR E 156 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N THR E 234 " --> pdb=" O CYS E 143 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N SER E 145 " --> pdb=" O THR E 234 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 182 through 183 Processing sheet with id=AC6, first strand: chain 'E' and resid 182 through 183 Processing sheet with id=AC7, first strand: chain 'E' and resid 242 through 244 Processing sheet with id=AC8, first strand: chain 'E' and resid 284 through 286 removed outlier: 3.538A pdb=" N PHE E 308 " --> pdb=" O ARG E 277 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.49 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4000 1.35 - 1.47: 3228 1.47 - 1.59: 5630 1.59 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 12916 Sorted by residual: bond pdb=" C1 NAG O 1 " pdb=" O5 NAG O 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.93e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.88e+00 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.24e+00 bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.22e+00 ... (remaining 12911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 17046 1.38 - 2.76: 532 2.76 - 4.15: 68 4.15 - 5.53: 14 5.53 - 6.91: 4 Bond angle restraints: 17664 Sorted by residual: angle pdb=" C GLY H 164 " pdb=" N THR H 165 " pdb=" CA THR H 165 " ideal model delta sigma weight residual 121.54 126.74 -5.20 1.91e+00 2.74e-01 7.41e+00 angle pdb=" C GLY D 164 " pdb=" N THR D 165 " pdb=" CA THR D 165 " ideal model delta sigma weight residual 121.54 126.71 -5.17 1.91e+00 2.74e-01 7.33e+00 angle pdb=" C HIS C 25 " pdb=" N SER C 26 " pdb=" CA SER C 26 " ideal model delta sigma weight residual 120.51 123.74 -3.23 1.45e+00 4.76e-01 4.95e+00 angle pdb=" C LEU C 251 " pdb=" N ASP C 252 " pdb=" CA ASP C 252 " ideal model delta sigma weight residual 122.46 125.52 -3.06 1.41e+00 5.03e-01 4.70e+00 angle pdb=" C LEU G 251 " pdb=" N ASP G 252 " pdb=" CA ASP G 252 " ideal model delta sigma weight residual 121.54 125.27 -3.73 1.91e+00 2.74e-01 3.81e+00 ... (remaining 17659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 7488 17.59 - 35.18: 438 35.18 - 52.76: 116 52.76 - 70.35: 23 70.35 - 87.94: 15 Dihedral angle restraints: 8080 sinusoidal: 3642 harmonic: 4438 Sorted by residual: dihedral pdb=" CB CYS G 46 " pdb=" SG CYS G 46 " pdb=" SG CYS G 89 " pdb=" CB CYS G 89 " ideal model delta sinusoidal sigma weight residual 93.00 43.91 49.09 1 1.00e+01 1.00e-02 3.31e+01 dihedral pdb=" CB CYS C 46 " pdb=" SG CYS C 46 " pdb=" SG CYS C 89 " pdb=" CB CYS C 89 " ideal model delta sinusoidal sigma weight residual 93.00 45.65 47.35 1 1.00e+01 1.00e-02 3.10e+01 dihedral pdb=" CB CYS C 116 " pdb=" SG CYS C 116 " pdb=" SG CYS C 127 " pdb=" CB CYS C 127 " ideal model delta sinusoidal sigma weight residual 93.00 54.73 38.27 1 1.00e+01 1.00e-02 2.06e+01 ... (remaining 8077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1627 0.046 - 0.091: 254 0.091 - 0.137: 139 0.137 - 0.182: 0 0.182 - 0.228: 2 Chirality restraints: 2022 Sorted by residual: chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN E 104 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN A 104 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA VAL E 290 " pdb=" N VAL E 290 " pdb=" C VAL E 290 " pdb=" CB VAL E 290 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 2019 not shown) Planarity restraints: 2246 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 66 " 0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO D 67 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 66 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.38e+00 pdb=" N PRO H 67 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO H 67 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 67 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 66 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.07e+00 pdb=" N PRO E 67 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO E 67 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 67 " -0.020 5.00e-02 4.00e+02 ... (remaining 2243 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3481 2.81 - 3.33: 10249 3.33 - 3.86: 19416 3.86 - 4.38: 20534 4.38 - 4.90: 37340 Nonbonded interactions: 91020 Sorted by model distance: nonbonded pdb=" OD1 ASP A 120 " pdb=" OG SER A 122 " model vdw 2.291 3.040 nonbonded pdb=" OD1 ASP G 197 " pdb=" OG1 THR G 200 " model vdw 2.329 3.040 nonbonded pdb=" OD1 ASP E 120 " pdb=" OG SER E 122 " model vdw 2.334 3.040 nonbonded pdb=" NH2 ARG C 245 " pdb=" OE1 GLN C 279 " model vdw 2.359 3.120 nonbonded pdb=" NH2 ARG G 245 " pdb=" OE1 GLN G 279 " model vdw 2.360 3.120 ... (remaining 91015 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 30.850 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12916 Z= 0.209 Angle : 0.528 6.910 17664 Z= 0.266 Chirality : 0.041 0.228 2022 Planarity : 0.004 0.047 2228 Dihedral : 12.375 87.938 5184 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.06 % Allowed : 8.45 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.21), residues: 1514 helix: 2.16 (0.30), residues: 250 sheet: -0.29 (0.25), residues: 456 loop : -2.42 (0.19), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP G 254 HIS 0.004 0.000 HIS G 83 PHE 0.004 0.000 PHE H 74 TYR 0.005 0.000 TYR C 136 ARG 0.001 0.000 ARG G 213 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 206 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 83 HIS cc_start: 0.4518 (m-70) cc_final: 0.4266 (m-70) REVERT: C 104 HIS cc_start: 0.7099 (m-70) cc_final: 0.6777 (m-70) REVERT: C 226 TRP cc_start: 0.8827 (p90) cc_final: 0.8561 (p90) REVERT: D 117 LEU cc_start: 0.7648 (tt) cc_final: 0.7446 (tt) REVERT: D 209 MET cc_start: 0.5983 (tpp) cc_final: 0.5263 (mtt) REVERT: A 57 LEU cc_start: 0.7672 (tp) cc_final: 0.7432 (mp) REVERT: G 83 HIS cc_start: 0.4061 (m170) cc_final: 0.3807 (m-70) REVERT: G 226 TRP cc_start: 0.8708 (p90) cc_final: 0.8409 (p90) REVERT: H 209 MET cc_start: 0.6323 (tpp) cc_final: 0.5666 (mtt) REVERT: E 57 LEU cc_start: 0.7761 (tp) cc_final: 0.7393 (mp) outliers start: 14 outliers final: 6 residues processed: 217 average time/residue: 0.2682 time to fit residues: 80.7423 Evaluate side-chains 142 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 136 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 282 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 0.0980 chunk 60 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 71 optimal weight: 0.0000 chunk 87 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN C 83 HIS C 265 HIS C 285 ASN D 105 GLN A 113 ASN A 196 HIS G 265 HIS G 285 ASN H 105 GLN H 175 HIS E 113 ASN E 196 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12916 Z= 0.191 Angle : 0.593 12.987 17664 Z= 0.287 Chirality : 0.045 0.295 2022 Planarity : 0.005 0.048 2228 Dihedral : 5.366 55.657 2342 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.09 % Allowed : 12.67 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.22), residues: 1514 helix: 3.03 (0.32), residues: 252 sheet: 0.30 (0.25), residues: 460 loop : -1.88 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 57 HIS 0.005 0.001 HIS C 265 PHE 0.010 0.001 PHE H 185 TYR 0.017 0.001 TYR H 49 ARG 0.007 0.000 ARG A 297 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 142 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.7251 (m-70) cc_final: 0.6966 (m-70) REVERT: C 117 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8021 (ptt-90) REVERT: C 226 TRP cc_start: 0.8883 (p90) cc_final: 0.8474 (p90) REVERT: D 201 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.6924 (m-30) REVERT: D 209 MET cc_start: 0.6088 (tpp) cc_final: 0.5485 (mtt) REVERT: A 57 LEU cc_start: 0.7967 (tp) cc_final: 0.7726 (mp) REVERT: G 103 LEU cc_start: 0.5096 (pp) cc_final: 0.4625 (mm) REVERT: G 104 HIS cc_start: 0.7139 (m-70) cc_final: 0.6719 (m-70) REVERT: G 226 TRP cc_start: 0.8721 (p90) cc_final: 0.8289 (p90) REVERT: H 201 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.6998 (m-30) REVERT: H 209 MET cc_start: 0.6255 (tpp) cc_final: 0.5866 (mtt) REVERT: E 57 LEU cc_start: 0.8047 (tp) cc_final: 0.7682 (mp) outliers start: 41 outliers final: 18 residues processed: 174 average time/residue: 0.1910 time to fit residues: 51.6213 Evaluate side-chains 146 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 125 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 189 HIS Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 285 ASN Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 282 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 40.0000 chunk 42 optimal weight: 0.0970 chunk 113 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 136 optimal weight: 0.9980 chunk 147 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 83 HIS G 100 GLN G 256 HIS H 53 GLN H 70 ASN H 106 ASN E 113 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12916 Z= 0.207 Angle : 0.581 10.964 17664 Z= 0.280 Chirality : 0.045 0.387 2022 Planarity : 0.004 0.055 2228 Dihedral : 5.232 55.517 2340 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.56 % Allowed : 14.10 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.22), residues: 1514 helix: 3.48 (0.32), residues: 246 sheet: 0.69 (0.25), residues: 454 loop : -1.65 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 57 HIS 0.003 0.001 HIS G 189 PHE 0.021 0.002 PHE E 266 TYR 0.013 0.001 TYR H 49 ARG 0.004 0.000 ARG A 297 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 123 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.7197 (m-70) cc_final: 0.6967 (m-70) REVERT: C 117 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7575 (ptt-90) REVERT: C 226 TRP cc_start: 0.8905 (p90) cc_final: 0.8528 (p90) REVERT: D 201 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7014 (m-30) REVERT: D 209 MET cc_start: 0.6103 (tpp) cc_final: 0.5543 (mtt) REVERT: A 57 LEU cc_start: 0.8073 (tp) cc_final: 0.7838 (mp) REVERT: G 246 TYR cc_start: 0.6031 (p90) cc_final: 0.5596 (p90) REVERT: H 201 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.6946 (m-30) REVERT: H 209 MET cc_start: 0.6243 (tpp) cc_final: 0.5995 (mtt) REVERT: E 57 LEU cc_start: 0.8155 (tp) cc_final: 0.7801 (mp) outliers start: 34 outliers final: 22 residues processed: 146 average time/residue: 0.1852 time to fit residues: 43.2149 Evaluate side-chains 137 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 112 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain H residue 70 ASN Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 282 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 91 optimal weight: 0.0040 chunk 136 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 129 optimal weight: 0.2980 chunk 39 optimal weight: 4.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 HIS C 285 ASN G 83 HIS G 285 ASN H 53 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12916 Z= 0.164 Angle : 0.551 10.078 17664 Z= 0.266 Chirality : 0.046 0.475 2022 Planarity : 0.004 0.053 2228 Dihedral : 5.216 54.109 2340 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.94 % Allowed : 14.93 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.22), residues: 1514 helix: 3.64 (0.32), residues: 246 sheet: 0.83 (0.25), residues: 450 loop : -1.44 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 210 HIS 0.004 0.000 HIS G 83 PHE 0.018 0.001 PHE E 266 TYR 0.010 0.001 TYR H 49 ARG 0.003 0.000 ARG A 297 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 115 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.7296 (m-70) cc_final: 0.7079 (m-70) REVERT: C 117 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7864 (ptt-90) REVERT: D 201 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7039 (m-30) REVERT: D 209 MET cc_start: 0.6157 (tpp) cc_final: 0.5574 (mtt) REVERT: A 57 LEU cc_start: 0.8080 (tp) cc_final: 0.7798 (mp) REVERT: G 246 TYR cc_start: 0.6105 (p90) cc_final: 0.5652 (p90) REVERT: H 201 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7001 (m-30) REVERT: H 209 MET cc_start: 0.6269 (tpp) cc_final: 0.6016 (mtt) REVERT: E 57 LEU cc_start: 0.8122 (tp) cc_final: 0.7712 (mp) outliers start: 39 outliers final: 26 residues processed: 142 average time/residue: 0.1830 time to fit residues: 41.2766 Evaluate side-chains 141 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 112 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 285 ASN Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 314 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 100 optimal weight: 0.1980 chunk 0 optimal weight: 40.0000 chunk 74 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 106 ASN G 83 HIS H 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12916 Z= 0.333 Angle : 0.677 9.314 17664 Z= 0.342 Chirality : 0.050 0.442 2022 Planarity : 0.005 0.067 2228 Dihedral : 5.531 54.429 2340 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.00 % Allowed : 15.99 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.22), residues: 1514 helix: 3.12 (0.31), residues: 244 sheet: 0.65 (0.24), residues: 474 loop : -1.48 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 293 HIS 0.007 0.001 HIS D 175 PHE 0.021 0.003 PHE C 243 TYR 0.017 0.002 TYR D 110 ARG 0.007 0.001 ARG D 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 105 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 117 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.7860 (ptt-90) REVERT: D 141 GLN cc_start: 0.8415 (tt0) cc_final: 0.8138 (mt0) REVERT: D 209 MET cc_start: 0.6508 (tpp) cc_final: 0.6098 (mtt) REVERT: A 57 LEU cc_start: 0.8199 (tp) cc_final: 0.7986 (mp) REVERT: A 268 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.7709 (p90) REVERT: G 246 TYR cc_start: 0.6008 (p90) cc_final: 0.5625 (p90) REVERT: H 209 MET cc_start: 0.6638 (tpp) cc_final: 0.6369 (mtt) REVERT: E 57 LEU cc_start: 0.8299 (tp) cc_final: 0.7953 (mp) REVERT: E 89 ARG cc_start: 0.6724 (mtm110) cc_final: 0.6494 (mtm110) outliers start: 53 outliers final: 32 residues processed: 149 average time/residue: 0.1905 time to fit residues: 45.1885 Evaluate side-chains 135 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 101 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 268 PHE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 314 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 120 optimal weight: 0.3980 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 139 optimal weight: 0.8980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 HIS C 285 ASN A 117 HIS G 83 HIS G 285 ASN H 141 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12916 Z= 0.269 Angle : 0.634 9.498 17664 Z= 0.314 Chirality : 0.049 0.558 2022 Planarity : 0.005 0.070 2228 Dihedral : 5.799 54.759 2340 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.24 % Allowed : 17.72 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.22), residues: 1514 helix: 2.92 (0.32), residues: 256 sheet: 0.63 (0.24), residues: 484 loop : -1.54 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 196 HIS 0.004 0.001 HIS D 52 PHE 0.016 0.002 PHE C 243 TYR 0.012 0.001 TYR H 110 ARG 0.004 0.000 ARG D 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 105 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 117 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8314 (ttt-90) REVERT: D 209 MET cc_start: 0.6509 (tpp) cc_final: 0.6126 (mtt) REVERT: A 57 LEU cc_start: 0.8231 (tp) cc_final: 0.8013 (mp) REVERT: G 103 LEU cc_start: 0.5032 (pp) cc_final: 0.4474 (mm) REVERT: G 246 TYR cc_start: 0.5975 (p90) cc_final: 0.5534 (p90) REVERT: H 201 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7582 (m-30) REVERT: E 57 LEU cc_start: 0.8296 (tp) cc_final: 0.7966 (mp) REVERT: E 268 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.7649 (p90) outliers start: 43 outliers final: 28 residues processed: 139 average time/residue: 0.1943 time to fit residues: 42.3859 Evaluate side-chains 130 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 99 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 268 PHE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 314 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 10.0000 chunk 82 optimal weight: 50.0000 chunk 105 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 285 ASN G 256 HIS G 285 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 12916 Z= 0.410 Angle : 0.745 10.059 17664 Z= 0.375 Chirality : 0.054 0.652 2022 Planarity : 0.006 0.084 2228 Dihedral : 6.215 59.587 2340 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 4.15 % Allowed : 17.35 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.22), residues: 1514 helix: 2.44 (0.32), residues: 258 sheet: 0.20 (0.23), residues: 498 loop : -1.61 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 196 HIS 0.008 0.001 HIS D 175 PHE 0.023 0.003 PHE G 243 TYR 0.018 0.002 TYR H 110 ARG 0.006 0.001 ARG D 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 95 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 117 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7487 (ptt-90) REVERT: C 260 SER cc_start: 0.8215 (p) cc_final: 0.7992 (t) REVERT: D 209 MET cc_start: 0.6674 (tpp) cc_final: 0.6418 (mtt) REVERT: A 57 LEU cc_start: 0.8246 (tp) cc_final: 0.8019 (mp) REVERT: A 268 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7754 (p90) REVERT: G 246 TYR cc_start: 0.5798 (p90) cc_final: 0.5460 (p90) REVERT: E 57 LEU cc_start: 0.8336 (tp) cc_final: 0.8011 (mp) REVERT: E 268 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.7685 (p90) outliers start: 55 outliers final: 41 residues processed: 145 average time/residue: 0.1855 time to fit residues: 42.6844 Evaluate side-chains 131 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 87 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 285 ASN Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 268 PHE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 314 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 28 optimal weight: 0.4980 chunk 91 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 113 optimal weight: 0.6980 chunk 131 optimal weight: 0.5980 chunk 138 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 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 285 ASN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 285 ASN H 53 GLN E 117 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12916 Z= 0.188 Angle : 0.629 8.859 17664 Z= 0.312 Chirality : 0.049 0.658 2022 Planarity : 0.004 0.067 2228 Dihedral : 6.104 58.264 2340 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.79 % Allowed : 18.63 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.22), residues: 1514 helix: 3.01 (0.32), residues: 254 sheet: 0.61 (0.24), residues: 476 loop : -1.60 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 196 HIS 0.003 0.001 HIS D 175 PHE 0.016 0.001 PHE E 266 TYR 0.011 0.001 TYR E 187 ARG 0.002 0.000 ARG G 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 95 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 201 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7520 (m-30) REVERT: D 209 MET cc_start: 0.6483 (tpp) cc_final: 0.5796 (mtt) REVERT: A 57 LEU cc_start: 0.8250 (tp) cc_final: 0.8003 (mp) REVERT: G 246 TYR cc_start: 0.5781 (p90) cc_final: 0.5500 (p90) REVERT: H 201 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7531 (m-30) REVERT: E 57 LEU cc_start: 0.8313 (tp) cc_final: 0.7977 (mp) outliers start: 37 outliers final: 21 residues processed: 125 average time/residue: 0.2077 time to fit residues: 40.4177 Evaluate side-chains 113 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 90 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 314 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 1.9990 chunk 138 optimal weight: 0.3980 chunk 81 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 88 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 chunk 86 optimal weight: 0.4980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 285 ASN D 175 HIS ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 285 ASN H 53 GLN H 175 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12916 Z= 0.194 Angle : 0.605 7.670 17664 Z= 0.303 Chirality : 0.049 0.641 2022 Planarity : 0.004 0.062 2228 Dihedral : 5.773 53.678 2340 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.64 % Allowed : 18.55 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.22), residues: 1514 helix: 3.15 (0.31), residues: 254 sheet: 0.66 (0.24), residues: 458 loop : -1.43 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 196 HIS 0.003 0.001 HIS D 175 PHE 0.013 0.002 PHE E 266 TYR 0.008 0.001 TYR H 49 ARG 0.004 0.000 ARG H 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 98 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 260 SER cc_start: 0.8211 (p) cc_final: 0.7966 (t) REVERT: D 201 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7443 (m-30) REVERT: D 209 MET cc_start: 0.6480 (tpp) cc_final: 0.5917 (mtt) REVERT: A 57 LEU cc_start: 0.8295 (tp) cc_final: 0.8036 (mp) REVERT: A 150 ASP cc_start: 0.8655 (p0) cc_final: 0.8429 (p0) REVERT: G 103 LEU cc_start: 0.4871 (pt) cc_final: 0.4392 (mm) REVERT: G 190 ASN cc_start: 0.6555 (OUTLIER) cc_final: 0.6305 (m-40) REVERT: G 246 TYR cc_start: 0.5717 (p90) cc_final: 0.5467 (p90) REVERT: H 201 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7461 (m-30) REVERT: E 57 LEU cc_start: 0.8322 (tp) cc_final: 0.7970 (mp) outliers start: 35 outliers final: 27 residues processed: 127 average time/residue: 0.2057 time to fit residues: 40.6755 Evaluate side-chains 124 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 94 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 190 ASN Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 285 ASN Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 314 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 149 optimal weight: 0.0770 chunk 137 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 285 ASN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 285 ASN H 175 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12916 Z= 0.359 Angle : 0.681 8.713 17664 Z= 0.344 Chirality : 0.053 0.685 2022 Planarity : 0.005 0.075 2228 Dihedral : 5.905 51.695 2340 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 2.64 % Allowed : 19.00 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.22), residues: 1514 helix: 2.80 (0.32), residues: 258 sheet: 0.49 (0.24), residues: 462 loop : -1.49 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 196 HIS 0.005 0.001 HIS A 193 PHE 0.020 0.002 PHE G 243 TYR 0.015 0.002 TYR H 110 ARG 0.006 0.001 ARG D 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 98 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 209 MET cc_start: 0.6557 (tpp) cc_final: 0.6346 (mtt) REVERT: A 57 LEU cc_start: 0.8295 (tp) cc_final: 0.8045 (mp) REVERT: G 246 TYR cc_start: 0.5720 (p90) cc_final: 0.5435 (p90) REVERT: H 201 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.7666 (m-30) REVERT: E 57 LEU cc_start: 0.8352 (tp) cc_final: 0.8012 (mp) outliers start: 35 outliers final: 29 residues processed: 129 average time/residue: 0.2046 time to fit residues: 41.8906 Evaluate side-chains 122 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 92 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 285 ASN Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 314 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 49 optimal weight: 0.0870 chunk 122 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 104 optimal weight: 0.4980 chunk 6 optimal weight: 30.0000 chunk 86 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 285 ASN D 175 HIS ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 285 ASN H 175 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.178366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.123800 restraints weight = 17385.473| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 3.69 r_work: 0.3331 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12916 Z= 0.180 Angle : 0.611 7.626 17664 Z= 0.306 Chirality : 0.049 0.595 2022 Planarity : 0.004 0.060 2228 Dihedral : 5.729 52.244 2340 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.56 % Allowed : 19.31 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.22), residues: 1514 helix: 3.07 (0.31), residues: 256 sheet: 0.65 (0.25), residues: 458 loop : -1.44 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 196 HIS 0.003 0.001 HIS D 52 PHE 0.012 0.001 PHE E 266 TYR 0.011 0.001 TYR H 49 ARG 0.002 0.000 ARG G 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2815.69 seconds wall clock time: 50 minutes 49.98 seconds (3049.98 seconds total)