Starting phenix.real_space_refine on Sun May 18 21:48:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vef_43172/05_2025/8vef_43172.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vef_43172/05_2025/8vef_43172.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vef_43172/05_2025/8vef_43172.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vef_43172/05_2025/8vef_43172.map" model { file = "/net/cci-nas-00/data/ceres_data/8vef_43172/05_2025/8vef_43172.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vef_43172/05_2025/8vef_43172.cif" } resolution = 3.04 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= 0.002 sd= 0.059 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 81 5.16 5 C 10990 2.51 5 N 2954 2.21 5 O 3529 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17554 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 3868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3868 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 21, 'TRANS': 464} Chain breaks: 2 Chain: "H" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 998 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "L" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 806 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "C" Number of atoms: 3868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3868 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 21, 'TRANS': 464} Chain breaks: 2 Chain: "J" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 998 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "K" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 806 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "E" Number of atoms: 3868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3868 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 21, 'TRANS': 464} Chain breaks: 2 Chain: "G" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 998 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "I" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 806 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: "V" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "W" 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: "C" 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 10.30, per 1000 atoms: 0.59 Number of scatterers: 17554 At special positions: 0 Unit cell: (125.628, 129.96, 154.869, 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 81 16.00 O 3529 8.00 N 2954 7.00 C 10990 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A1137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS C1047 " distance=2.04 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 284 " distance=2.02 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 77 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 145 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A1047 " - pdb=" SG CYS E 30 " distance=2.04 Simple disulfide: pdb=" SG CYS A1144 " - pdb=" SG CYS A1148 " distance=2.03 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 30 " - pdb=" SG CYS E1047 " distance=2.04 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 284 " distance=2.02 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 77 " distance=2.03 Simple disulfide: pdb=" SG CYS C 100 " - pdb=" SG CYS C 145 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 312 " distance=2.03 Simple disulfide: pdb=" SG CYS C1144 " - pdb=" SG CYS C1148 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 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 284 " distance=2.02 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS E 100 " - pdb=" SG CYS E 145 " distance=2.03 Simple disulfide: pdb=" SG CYS E 288 " - pdb=" SG CYS E 312 " distance=2.03 Simple disulfide: pdb=" SG CYS E1144 " - pdb=" SG CYS E1148 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 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 ALPHA1-3 " BMA O 3 " - " MAN O 6 " " BMA S 3 " - " MAN S 6 " " BMA V 3 " - " MAN V 6 " ALPHA1-6 " BMA O 3 " - " MAN O 4 " " MAN O 4 " - " MAN O 5 " " BMA S 3 " - " MAN S 4 " " MAN S 4 " - " MAN S 5 " " BMA V 3 " - " MAN V 4 " " MAN V 4 " - " MAN V 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " 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 S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A2001 " - " ASN A 21 " " NAG A2002 " - " ASN A 33 " " NAG C2001 " - " ASN C 21 " " NAG C2002 " - " ASN C 33 " " NAG E2001 " - " ASN E 21 " " NAG E2002 " - " ASN E 33 " " NAG E2003 " - " ASN E 83 " " NAG M 1 " - " ASN A 97 " " NAG N 1 " - " ASN A 83 " " NAG O 1 " - " ASN A 169 " " NAG P 1 " - " ASN A1154 " " NAG Q 1 " - " ASN C 97 " " NAG R 1 " - " ASN C 83 " " NAG S 1 " - " ASN C 169 " " NAG T 1 " - " ASN C1154 " " NAG U 1 " - " ASN E 97 " " NAG V 1 " - " ASN E 169 " " NAG W 1 " - " ASN E1154 " Time building additional restraints: 4.52 Conformation dependent library (CDL) restraints added in 2.0 seconds 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3966 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 42 sheets defined 21.0% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain 'A' and resid 66 through 73 Processing helix chain 'A' and resid 77 through 81 removed outlier: 3.535A pdb=" N LEU A 80 " --> pdb=" O CYS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 117 removed outlier: 4.183A pdb=" N SER A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 133 removed outlier: 3.937A pdb=" N TRP A 133 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 removed outlier: 3.571A pdb=" N GLN A 197 " --> pdb=" O ASN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1059 removed outlier: 3.715A pdb=" N MET A1059 " --> pdb=" O VAL A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1127 removed outlier: 3.703A pdb=" N LEU A1089 " --> pdb=" O ASP A1085 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP A1090 " --> pdb=" O ASP A1086 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A1091 " --> pdb=" O GLY A1087 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU A1105 " --> pdb=" O LEU A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1155 removed outlier: 3.672A pdb=" N GLY A1155 " --> pdb=" O SER A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1162 through 1172 removed outlier: 3.910A pdb=" N SER A1166 " --> pdb=" O TYR A1162 " (cutoff:3.500A) Processing helix chain 'H' and resid 100H through 100M removed outlier: 3.900A pdb=" N ALA H 100L" --> pdb=" O ALA H 100I" (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE H 100M" --> pdb=" O ASP H 100J" (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.100A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 73 Processing helix chain 'C' and resid 77 through 81 Processing helix chain 'C' and resid 107 through 117 removed outlier: 4.293A pdb=" N SER C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 133 removed outlier: 4.092A pdb=" N TRP C 133 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 202 Processing helix chain 'C' and resid 1037 through 1059 removed outlier: 3.804A pdb=" N MET C1059 " --> pdb=" O VAL C1055 " (cutoff:3.500A) Processing helix chain 'C' and resid 1074 through 1127 removed outlier: 3.675A pdb=" N LEU C1089 " --> pdb=" O ASP C1085 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP C1090 " --> pdb=" O ASP C1086 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE C1091 " --> pdb=" O GLY C1087 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1145 through 1155 removed outlier: 3.654A pdb=" N GLY C1155 " --> pdb=" O SER C1151 " (cutoff:3.500A) Processing helix chain 'C' and resid 1162 through 1172 removed outlier: 3.828A pdb=" N SER C1166 " --> pdb=" O TYR C1162 " (cutoff:3.500A) Processing helix chain 'J' and resid 100I through 100M Processing helix chain 'K' and resid 79 through 83 removed outlier: 4.142A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 73 Processing helix chain 'E' and resid 77 through 81 Processing helix chain 'E' and resid 107 through 117 removed outlier: 4.245A pdb=" N SER E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 133 removed outlier: 4.156A pdb=" N TRP E 133 " --> pdb=" O LYS E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 202 removed outlier: 3.559A pdb=" N GLN E 197 " --> pdb=" O ASN E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 1037 through 1059 removed outlier: 3.733A pdb=" N MET E1059 " --> pdb=" O VAL E1055 " (cutoff:3.500A) Processing helix chain 'E' and resid 1074 through 1127 removed outlier: 3.749A pdb=" N LEU E1089 " --> pdb=" O ASP E1085 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP E1090 " --> pdb=" O ASP E1086 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE E1091 " --> pdb=" O GLY E1087 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU E1105 " --> pdb=" O LEU E1101 " (cutoff:3.500A) Processing helix chain 'E' and resid 1145 through 1155 removed outlier: 3.718A pdb=" N GLY E1155 " --> pdb=" O SER E1151 " (cutoff:3.500A) Processing helix chain 'E' and resid 1159 through 1161 No H-bonds generated for 'chain 'E' and resid 1159 through 1161' Processing helix chain 'E' and resid 1162 through 1172 removed outlier: 3.927A pdb=" N SER E1166 " --> pdb=" O TYR E1162 " (cutoff:3.500A) Processing helix chain 'G' and resid 100H through 100M removed outlier: 3.850A pdb=" N ALA G 100L" --> pdb=" O ALA G 100I" (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE G 100M" --> pdb=" O ASP G 100J" (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 removed outlier: 4.134A pdb=" N PHE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1032 through 1034 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 removed outlier: 4.190A pdb=" N ASP A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) 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 60 through 61 removed outlier: 6.348A pdb=" N LEU A 60 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.848A pdb=" N ARG A 84 " --> pdb=" O PHE A 121 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE A 121 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER A 120 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU A 181 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 157 through 159 Processing sheet with id=AA7, first strand: chain 'A' and resid 170 through 175 Processing sheet with id=AA8, first strand: chain 'A' and resid 293 through 295 removed outlier: 4.063A pdb=" N CYS A 288 " --> pdb=" O ILE A 295 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.661A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TYR H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.395A pdb=" N TRP H 35A" --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.661A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TYR H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.395A pdb=" N TRP H 35A" --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.828A pdb=" N SER L 7 " --> pdb=" O THR L 22 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.680A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 1032 through 1034 removed outlier: 3.503A pdb=" N GLY C 16 " --> pdb=" O GLY C1023 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 24 through 26 removed outlier: 4.208A pdb=" N ASP C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB9, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC1, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.699A pdb=" N LEU C 60 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE C 89 " --> pdb=" O ILE C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.949A pdb=" N ARG C 84 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE C 121 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER C 120 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR C 262 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEU C 185 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU C 181 " --> pdb=" O LEU C 266 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 157 through 159 Processing sheet with id=AC4, first strand: chain 'C' and resid 170 through 175 Processing sheet with id=AC5, first strand: chain 'C' and resid 293 through 295 removed outlier: 3.534A pdb=" N ILE C 295 " --> pdb=" O CYS C 288 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N CYS C 288 " --> pdb=" O ILE C 295 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AC7, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.736A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TYR J 50 " --> pdb=" O TRP J 35A" (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP J 35A" --> pdb=" O TYR J 50 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.830A pdb=" N SER K 7 " --> pdb=" O THR K 22 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N THR K 22 " --> pdb=" O SER K 7 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 10 through 11 removed outlier: 3.545A pdb=" N THR K 102 " --> pdb=" O TYR K 86 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 1032 through 1034 Processing sheet with id=AD2, first strand: chain 'E' and resid 24 through 26 removed outlier: 4.111A pdb=" N ASP E 24 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AD4, first strand: chain 'E' and resid 60 through 61 removed outlier: 6.612A pdb=" N LEU E 60 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE E 89 " --> pdb=" O ILE E 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.959A pdb=" N ARG E 84 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE E 121 " --> pdb=" O ARG E 84 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N SER E 267 " --> pdb=" O SER E 119 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE E 121 " --> pdb=" O ALA E 265 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ALA E 265 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ARG E 123 " --> pdb=" O ALA E 263 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA E 263 " --> pdb=" O ARG E 123 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR E 262 " --> pdb=" O LEU E 185 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N LEU E 185 " --> pdb=" O TYR E 262 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU E 181 " --> pdb=" O LEU E 266 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 142 through 146 removed outlier: 4.563A pdb=" N CYS E 145 " --> pdb=" O SER E 152 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 157 through 159 Processing sheet with id=AD8, first strand: chain 'E' and resid 170 through 175 Processing sheet with id=AD9, first strand: chain 'E' and resid 293 through 295 removed outlier: 4.088A pdb=" N CYS E 288 " --> pdb=" O ILE E 295 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 301 through 302 Processing sheet with id=AE2, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.689A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR G 50 " --> pdb=" O TRP G 35A" (cutoff:3.500A) removed outlier: 6.349A pdb=" N TRP G 35A" --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.689A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR G 50 " --> pdb=" O TRP G 35A" (cutoff:3.500A) removed outlier: 6.349A pdb=" N TRP G 35A" --> pdb=" O TYR G 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.813A pdb=" N SER I 7 " --> pdb=" O THR I 22 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N THR I 22 " --> pdb=" O SER I 7 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.509A pdb=" N THR I 102 " --> pdb=" O TYR I 86 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) 669 hydrogen bonds defined for protein. 1818 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: 5.64 Time building geometry restraints manager: 5.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5390 1.34 - 1.46: 4289 1.46 - 1.58: 8175 1.58 - 1.70: 0 1.70 - 1.83: 108 Bond restraints: 17962 Sorted by residual: bond pdb=" N ILE L 29 " pdb=" CA ILE L 29 " ideal model delta sigma weight residual 1.460 1.500 -0.040 1.10e-02 8.26e+03 1.34e+01 bond pdb=" N ILE I 29 " pdb=" CA ILE I 29 " ideal model delta sigma weight residual 1.460 1.499 -0.040 1.10e-02 8.26e+03 1.30e+01 bond pdb=" N ILE H 51 " pdb=" CA ILE H 51 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.11e-02 8.12e+03 1.23e+01 bond pdb=" N ILE K 29 " pdb=" CA ILE K 29 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.10e-02 8.26e+03 1.18e+01 bond pdb=" N LYS J 64 " pdb=" CA LYS J 64 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.12e-02 7.97e+03 1.15e+01 ... (remaining 17957 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 23431 2.36 - 4.71: 806 4.71 - 7.07: 104 7.07 - 9.43: 22 9.43 - 11.78: 2 Bond angle restraints: 24365 Sorted by residual: angle pdb=" C TYR J 35 " pdb=" CA TYR J 35 " pdb=" CB TYR J 35 " ideal model delta sigma weight residual 110.19 98.41 11.78 1.64e+00 3.72e-01 5.16e+01 angle pdb=" C TYR J 53 " pdb=" CA TYR J 53 " pdb=" CB TYR J 53 " ideal model delta sigma weight residual 110.88 101.51 9.37 1.57e+00 4.06e-01 3.56e+01 angle pdb=" CA TYR J 100F" pdb=" C TYR J 100F" pdb=" O TYR J 100F" ideal model delta sigma weight residual 120.49 113.95 6.54 1.16e+00 7.43e-01 3.18e+01 angle pdb=" N GLY H 100G" pdb=" CA GLY H 100G" pdb=" C GLY H 100G" ideal model delta sigma weight residual 112.49 118.71 -6.22 1.21e+00 6.83e-01 2.65e+01 angle pdb=" CA TYR J 35 " pdb=" C TYR J 35 " pdb=" O TYR J 35 " ideal model delta sigma weight residual 120.32 114.72 5.60 1.10e+00 8.26e-01 2.59e+01 ... (remaining 24360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.56: 10479 20.56 - 41.13: 605 41.13 - 61.69: 80 61.69 - 82.26: 33 82.26 - 102.82: 14 Dihedral angle restraints: 11211 sinusoidal: 4980 harmonic: 6231 Sorted by residual: dihedral pdb=" C TYR J 35 " pdb=" N TYR J 35 " pdb=" CA TYR J 35 " pdb=" CB TYR J 35 " ideal model delta harmonic sigma weight residual -122.60 -105.22 -17.38 0 2.50e+00 1.60e-01 4.83e+01 dihedral pdb=" C TYR H 100D" pdb=" N TYR H 100D" pdb=" CA TYR H 100D" pdb=" CB TYR H 100D" ideal model delta harmonic sigma weight residual -122.60 -136.55 13.95 0 2.50e+00 1.60e-01 3.12e+01 dihedral pdb=" C GLU E 283 " pdb=" N GLU E 283 " pdb=" CA GLU E 283 " pdb=" CB GLU E 283 " ideal model delta harmonic sigma weight residual -122.60 -135.68 13.08 0 2.50e+00 1.60e-01 2.74e+01 ... (remaining 11208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2367 0.093 - 0.186: 301 0.186 - 0.279: 33 0.279 - 0.372: 9 0.372 - 0.465: 6 Chirality restraints: 2716 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.19e+01 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.03e+01 chirality pdb=" CA TYR J 35 " pdb=" N TYR J 35 " pdb=" C TYR J 35 " pdb=" CB TYR J 35 " both_signs ideal model delta sigma weight residual False 2.51 2.98 -0.47 2.00e-01 2.50e+01 5.42e+00 ... (remaining 2713 not shown) Planarity restraints: 3119 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 1 " -0.243 2.00e-02 2.50e+03 2.08e-01 5.42e+02 pdb=" C7 NAG R 1 " 0.052 2.00e-02 2.50e+03 pdb=" C8 NAG R 1 " 0.028 2.00e-02 2.50e+03 pdb=" N2 NAG R 1 " 0.347 2.00e-02 2.50e+03 pdb=" O7 NAG R 1 " -0.184 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " -0.133 2.00e-02 2.50e+03 1.13e-01 1.59e+02 pdb=" C7 NAG N 1 " 0.026 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " 0.031 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " 0.181 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " -0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E2003 " -0.085 2.00e-02 2.50e+03 7.02e-02 6.16e+01 pdb=" C7 NAG E2003 " 0.023 2.00e-02 2.50e+03 pdb=" C8 NAG E2003 " -0.064 2.00e-02 2.50e+03 pdb=" N2 NAG E2003 " 0.112 2.00e-02 2.50e+03 pdb=" O7 NAG E2003 " 0.014 2.00e-02 2.50e+03 ... (remaining 3116 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4954 2.82 - 3.34: 13592 3.34 - 3.86: 27839 3.86 - 4.38: 31064 4.38 - 4.90: 56622 Nonbonded interactions: 134071 Sorted by model distance: nonbonded pdb=" OE1 GLU C 44 " pdb=" OG SER C 297 " model vdw 2.299 3.040 nonbonded pdb=" OE1 GLU A 44 " pdb=" OG SER A 297 " model vdw 2.312 3.040 nonbonded pdb=" OG1 THR K 69 " pdb=" OE1 GLU K 70 " model vdw 2.322 3.040 nonbonded pdb=" OG1 THR I 69 " pdb=" OE1 GLU I 70 " model vdw 2.327 3.040 nonbonded pdb=" OG1 THR L 69 " pdb=" OE1 GLU L 70 " model vdw 2.328 3.040 ... (remaining 134066 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 'C' selection = (chain 'E' and (resid 11 through 1173 or resid 2001 through 2002)) } 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 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'O' selection = chain 'S' selection = chain 'V' } 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: 2.260 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: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 39.630 Find NCS groups from input model: 0.710 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 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 : 0.006 0.054 18030 Z= 0.326 Angle : 0.984 11.783 24542 Z= 0.571 Chirality : 0.066 0.465 2716 Planarity : 0.009 0.208 3101 Dihedral : 13.574 102.822 7164 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.05 % Allowed : 0.32 % Favored : 99.63 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 3.23 % 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: -0.53 (0.17), residues: 2127 helix: 0.78 (0.26), residues: 360 sheet: 1.42 (0.22), residues: 519 loop : -1.59 (0.15), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 86 HIS 0.006 0.001 HIS E 18 PHE 0.032 0.003 PHE J 97 TYR 0.051 0.003 TYR J 53 ARG 0.014 0.001 ARG E 317 Details of bonding type rmsd link_NAG-ASN : bond 0.00506 ( 18) link_NAG-ASN : angle 2.89302 ( 54) link_ALPHA1-6 : bond 0.00553 ( 6) link_ALPHA1-6 : angle 1.22677 ( 18) link_BETA1-4 : bond 0.00858 ( 14) link_BETA1-4 : angle 1.74397 ( 42) link_ALPHA1-3 : bond 0.00387 ( 3) link_ALPHA1-3 : angle 1.54933 ( 9) hydrogen bonds : bond 0.16786 ( 643) hydrogen bonds : angle 7.26745 ( 1818) SS BOND : bond 0.00672 ( 27) SS BOND : angle 1.54004 ( 54) covalent geometry : bond 0.00605 (17962) covalent geometry : angle 0.97127 (24365) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 284 time to evaluate : 1.848 Fit side-chains revert: symmetry clash REVERT: A 53 ARG cc_start: 0.7126 (tpp80) cc_final: 0.6771 (mtt90) REVERT: E 270 PRO cc_start: 0.7100 (Cg_endo) cc_final: 0.6900 (Cg_exo) REVERT: E 1027 GLN cc_start: 0.7992 (tp40) cc_final: 0.7701 (tt0) REVERT: G 22 CYS cc_start: 0.5783 (t) cc_final: 0.5560 (t) REVERT: I 33 LEU cc_start: 0.9065 (tp) cc_final: 0.8864 (tp) outliers start: 1 outliers final: 0 residues processed: 284 average time/residue: 0.3030 time to fit residues: 126.4106 Evaluate side-chains 163 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.850 ------------------------------------------------------------------------------- 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: 4.9990 chunk 159 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 190 optimal weight: 8.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A1026 HIS A1117 ASN A1125 GLN H 76 ASN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1026 HIS C1125 GLN ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN E 214 ASN E1026 HIS E1124 ASN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.158792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.103306 restraints weight = 20784.613| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.93 r_work: 0.3061 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 18030 Z= 0.215 Angle : 0.637 10.148 24542 Z= 0.333 Chirality : 0.046 0.196 2716 Planarity : 0.005 0.063 3101 Dihedral : 8.188 76.969 3192 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.59 % Allowed : 6.88 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.32 (0.17), residues: 2127 helix: 1.88 (0.27), residues: 363 sheet: 0.97 (0.21), residues: 561 loop : -1.58 (0.15), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1092 HIS 0.007 0.002 HIS A1026 PHE 0.025 0.003 PHE G 78 TYR 0.025 0.002 TYR J 35 ARG 0.007 0.001 ARG C 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 18) link_NAG-ASN : angle 2.17862 ( 54) link_ALPHA1-6 : bond 0.00532 ( 6) link_ALPHA1-6 : angle 1.82647 ( 18) link_BETA1-4 : bond 0.00563 ( 14) link_BETA1-4 : angle 1.38869 ( 42) link_ALPHA1-3 : bond 0.01123 ( 3) link_ALPHA1-3 : angle 2.61411 ( 9) hydrogen bonds : bond 0.06565 ( 643) hydrogen bonds : angle 5.40185 ( 1818) SS BOND : bond 0.00576 ( 27) SS BOND : angle 1.06887 ( 54) covalent geometry : bond 0.00524 (17962) covalent geometry : angle 0.62261 (24365) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 169 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 4 MET cc_start: 0.7322 (mmp) cc_final: 0.6942 (mmp) REVERT: C 53 ARG cc_start: 0.7496 (mtt90) cc_final: 0.7190 (ttm110) REVERT: E 281 LEU cc_start: 0.8707 (tp) cc_final: 0.8468 (tp) REVERT: E 1017 MET cc_start: 0.8914 (ttp) cc_final: 0.8551 (ttm) REVERT: E 1077 MET cc_start: 0.8600 (tpp) cc_final: 0.8181 (ttm) REVERT: I 33 LEU cc_start: 0.8538 (tp) cc_final: 0.8180 (tp) REVERT: I 49 TYR cc_start: 0.7536 (m-80) cc_final: 0.7220 (m-80) outliers start: 11 outliers final: 7 residues processed: 176 average time/residue: 0.3073 time to fit residues: 80.9422 Evaluate side-chains 158 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 151 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain J residue 5 GLN Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 275 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.804 > 50: distance: 61 - 68: 3.014 distance: 83 - 85: 16.862 distance: 85 - 86: 13.063 distance: 85 - 91: 12.156 distance: 86 - 87: 19.520 distance: 86 - 89: 21.175 distance: 87 - 88: 16.930 distance: 87 - 92: 36.852 distance: 89 - 90: 23.236 distance: 90 - 91: 22.750 distance: 92 - 93: 38.113 distance: 93 - 94: 33.022 distance: 94 - 95: 51.048 distance: 94 - 96: 28.420 distance: 96 - 97: 13.447 distance: 97 - 98: 24.290 distance: 97 - 100: 29.646 distance: 98 - 99: 24.665 distance: 98 - 102: 25.938 distance: 100 - 101: 15.791 distance: 102 - 103: 28.596 distance: 103 - 104: 24.784 distance: 104 - 105: 20.554 distance: 104 - 106: 27.515 distance: 106 - 107: 22.241 distance: 107 - 108: 25.395 distance: 107 - 110: 23.083 distance: 108 - 109: 17.269 distance: 108 - 114: 14.846 distance: 110 - 111: 12.394 distance: 110 - 112: 20.946 distance: 111 - 113: 14.136 distance: 114 - 115: 6.132 distance: 115 - 116: 23.674 distance: 115 - 118: 12.569 distance: 116 - 117: 23.231 distance: 116 - 122: 30.117 distance: 118 - 119: 10.457 distance: 118 - 120: 12.725 distance: 119 - 121: 7.927 distance: 122 - 123: 22.714 distance: 123 - 124: 19.353 distance: 123 - 126: 19.716 distance: 124 - 125: 23.162 distance: 124 - 129: 37.128 distance: 126 - 128: 9.235 distance: 129 - 130: 14.802 distance: 130 - 131: 7.379 distance: 130 - 133: 22.866 distance: 131 - 132: 15.843 distance: 131 - 135: 42.722 distance: 133 - 134: 22.802 distance: 135 - 136: 19.164 distance: 136 - 137: 13.447 distance: 136 - 139: 27.979 distance: 137 - 138: 39.191 distance: 137 - 143: 17.553 distance: 139 - 140: 25.716 distance: 140 - 141: 14.114 distance: 140 - 142: 3.708 distance: 143 - 144: 5.591 distance: 144 - 145: 33.396 distance: 144 - 147: 20.316 distance: 145 - 146: 4.494 distance: 145 - 148: 21.201