Starting phenix.real_space_refine on Wed Jun 18 19:04:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k3a_22654/06_2025/7k3a_22654.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k3a_22654/06_2025/7k3a_22654.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k3a_22654/06_2025/7k3a_22654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k3a_22654/06_2025/7k3a_22654.map" model { file = "/net/cci-nas-00/data/ceres_data/7k3a_22654/06_2025/7k3a_22654.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k3a_22654/06_2025/7k3a_22654.cif" } resolution = 4.2 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= 0.005 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 99 5.16 5 C 13359 2.51 5 N 3618 2.21 5 O 4350 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21426 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "B" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1353 Classifications: {'peptide': 165} Link IDs: {'TRANS': 164} Chain: "C" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "D" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1353 Classifications: {'peptide': 165} Link IDs: {'TRANS': 164} Chain: "E" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "F" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1353 Classifications: {'peptide': 165} Link IDs: {'TRANS': 164} Chain: "G" Number of atoms: 1502 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 202, 1501 Classifications: {'peptide': 202} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "A" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1528 Chain: "H" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1608 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Chain: "I" Number of atoms: 1502 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 202, 1501 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "A" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1528 Chain: "J" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1608 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Chain: "K" Number of atoms: 1502 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 202, 1501 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "A" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1528 Chain: "L" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1608 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 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: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 16.93, per 1000 atoms: 0.79 Number of scatterers: 21426 At special positions: 0 Unit cell: (183.54, 183.54, 144.97, 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 99 16.00 O 4350 8.00 N 3618 7.00 C 13359 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.32 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.02 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=1.83 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.02 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=1.93 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.02 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.04 Simple disulfide: pdb=" SG CYS G 139 " - pdb=" SG CYS G 199 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.04 Simple disulfide: pdb=" SG CYS I 139 " - pdb=" SG CYS I 199 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 150 " - pdb=" SG CYS J 206 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.04 Simple disulfide: pdb=" SG CYS K 139 " - pdb=" SG CYS K 199 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 150 " - pdb=" SG CYS L 206 " 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 ALPHA1-2 " MAN O 5 " - " MAN O 6 " " MAN R 5 " - " MAN R 6 " " MAN U 5 " - " MAN U 6 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 8 " " MAN O 4 " - " MAN O 7 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 8 " " MAN R 4 " - " MAN R 7 " " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 8 " " MAN U 4 " - " MAN U 7 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " " BMA O 3 " - " MAN O 4 " " MAN O 4 " - " MAN O 5 " " BMA Q 3 " - " MAN Q 5 " " BMA R 3 " - " MAN R 4 " " MAN R 4 " - " MAN R 5 " " BMA T 3 " - " MAN T 5 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " 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 Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " NAG-ASN " NAG A 401 " - " ASN A 22 " " NAG A 402 " - " ASN A 81 " " NAG B 301 " - " ASN B 154 " " NAG C 401 " - " ASN C 22 " " NAG C 402 " - " ASN C 81 " " NAG D 301 " - " ASN D 154 " " NAG E 401 " - " ASN E 22 " " NAG E 402 " - " ASN E 81 " " NAG F 301 " - " ASN F 154 " " NAG M 1 " - " ASN A 38 " " NAG N 1 " - " ASN A 165 " " NAG O 1 " - " ASN A 285 " " NAG P 1 " - " ASN C 38 " " NAG Q 1 " - " ASN C 165 " " NAG R 1 " - " ASN C 285 " " NAG S 1 " - " ASN E 38 " " NAG T 1 " - " ASN E 165 " " NAG U 1 " - " ASN E 285 " Time building additional restraints: 7.13 Conformation dependent library (CDL) restraints added in 2.7 seconds 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4932 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 63 sheets defined 19.1% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 5.246A pdb=" N VAL A 78 " --> pdb=" O HIS A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'B' and resid 38 through 50 removed outlier: 4.322A pdb=" N GLY B 50 " --> pdb=" O ASP B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 126 Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 162 through 172 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 5.246A pdb=" N VAL C 78 " --> pdb=" O HIS C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'D' and resid 38 through 50 removed outlier: 4.323A pdb=" N GLY D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 126 Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 162 through 172 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 80 removed outlier: 5.246A pdb=" N VAL E 78 " --> pdb=" O HIS E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 116 Processing helix chain 'E' and resid 187 through 195 Processing helix chain 'F' and resid 38 through 50 removed outlier: 4.322A pdb=" N GLY F 50 " --> pdb=" O ASP F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 126 Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 159 through 161 No H-bonds generated for 'chain 'F' and resid 159 through 161' Processing helix chain 'F' and resid 162 through 172 Processing helix chain 'G' and resid 81 through 85 Processing helix chain 'G' and resid 126 through 133 Processing helix chain 'G' and resid 187 through 192 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.517A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 110 Processing helix chain 'H' and resid 197 through 202 Processing helix chain 'I' and resid 81 through 85 Processing helix chain 'I' and resid 126 through 132 Processing helix chain 'I' and resid 188 through 192 Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 62 through 65 Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.516A pdb=" N ASP J 90 " --> pdb=" O ARG J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 110 Processing helix chain 'J' and resid 197 through 202 Processing helix chain 'K' and resid 81 through 85 Processing helix chain 'K' and resid 126 through 132 Processing helix chain 'K' and resid 188 through 194 Processing helix chain 'L' and resid 28 through 32 Processing helix chain 'L' and resid 62 through 65 Processing helix chain 'L' and resid 87 through 91 removed outlier: 3.516A pdb=" N ASP L 90 " --> pdb=" O ARG L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 110 Processing helix chain 'L' and resid 197 through 202 Processing sheet with id=AA1, first strand: chain 'B' and resid 33 through 37 removed outlier: 4.830A pdb=" N TYR B 22 " --> pdb=" O ASP B 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 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 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 5.768A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N CYS A 277 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN A 53 " --> pdb=" O CYS A 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 61 Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 101 removed outlier: 6.952A pdb=" N ASP A 101 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N TRP A 234 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 100 through 101 removed outlier: 6.952A pdb=" N ASP A 101 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N TRP A 234 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB1, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.553A pdb=" N ALA A 138 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 10.557A pdb=" N GLY A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB3, first strand: chain 'A' and resid 286 through 288 removed outlier: 4.135A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 33 through 37 removed outlier: 4.829A pdb=" N TYR D 22 " --> pdb=" O ASP D 37 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY D 23 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY C 16 " --> pdb=" O GLY D 23 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AB6, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB7, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB8, first strand: chain 'C' and resid 51 through 54 removed outlier: 5.768A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N CYS C 277 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN C 53 " --> pdb=" O CYS C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 58 through 61 Processing sheet with id=AC1, first strand: chain 'C' and resid 100 through 101 removed outlier: 6.953A pdb=" N ASP C 101 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 100 through 101 removed outlier: 6.953A pdb=" N ASP C 101 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC4, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.555A pdb=" N ALA C 138 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 10.557A pdb=" N GLY C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC6, first strand: chain 'C' and resid 286 through 288 removed outlier: 4.134A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 33 through 37 removed outlier: 4.829A pdb=" N TYR F 22 " --> pdb=" O ASP F 37 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY E 16 " --> pdb=" O GLY F 23 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AC9, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AD1, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AD2, first strand: chain 'E' and resid 51 through 54 removed outlier: 5.768A pdb=" N ILE E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N CYS E 277 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN E 53 " --> pdb=" O CYS E 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 58 through 61 Processing sheet with id=AD4, first strand: chain 'E' and resid 100 through 101 removed outlier: 6.952A pdb=" N ASP E 101 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N TRP E 234 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ILE E 179 " --> pdb=" O GLY E 256 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY E 256 " --> pdb=" O ILE E 179 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 100 through 101 removed outlier: 6.952A pdb=" N ASP E 101 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N TRP E 234 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD7, first strand: chain 'E' and resid 136 through 141 removed outlier: 7.554A pdb=" N ALA E 138 " --> pdb=" O GLY E 144 " (cutoff:3.500A) removed outlier: 10.556A pdb=" N GLY E 144 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD9, first strand: chain 'E' and resid 286 through 288 removed outlier: 4.133A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.193A pdb=" N TRP G 37 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=AE3, first strand: chain 'G' and resid 119 through 123 removed outlier: 5.659A pdb=" N TYR G 178 " --> pdb=" O ASN G 143 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER G 179 " --> pdb=" O THR G 169 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 149 through 155 removed outlier: 4.135A pdb=" N LYS G 150 " --> pdb=" O THR G 202 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.317A pdb=" N GLU H 10 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.317A pdb=" N GLU H 10 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 130 through 134 removed outlier: 6.090A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N SER H 187 " --> pdb=" O ALA H 178 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA H 178 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER H 189 " --> pdb=" O PHE H 176 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 160 through 164 Processing sheet with id=AF1, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.372A pdb=" N TRP I 37 " --> pdb=" O LEU I 49 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AF3, first strand: chain 'I' and resid 119 through 123 removed outlier: 3.557A pdb=" N VAL I 138 " --> pdb=" O PHE I 123 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N TYR I 178 " --> pdb=" O ASN I 143 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 150 through 155 Processing sheet with id=AF5, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AF6, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.318A pdb=" N GLU J 10 " --> pdb=" O THR J 123 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.318A pdb=" N GLU J 10 " --> pdb=" O THR J 123 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL J 115 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 130 through 134 removed outlier: 6.090A pdb=" N TYR J 186 " --> pdb=" O ASP J 154 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N SER J 187 " --> pdb=" O ALA J 178 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA J 178 " --> pdb=" O SER J 187 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER J 189 " --> pdb=" O PHE J 176 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 160 through 164 Processing sheet with id=AG1, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.607A pdb=" N GLY K 12 " --> pdb=" O THR K 109 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TRP K 37 " --> pdb=" O LEU K 49 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AG3, first strand: chain 'K' and resid 119 through 123 removed outlier: 3.978A pdb=" N VAL K 138 " --> pdb=" O PHE K 123 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N TYR K 178 " --> pdb=" O ASN K 143 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 158 through 159 removed outlier: 3.999A pdb=" N CYS K 199 " --> pdb=" O LYS K 212 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS K 212 " --> pdb=" O CYS K 199 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 3 through 6 Processing sheet with id=AG6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.318A pdb=" N GLU L 10 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ARG L 38 " --> pdb=" O TRP L 47 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TRP L 47 " --> pdb=" O ARG L 38 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.318A pdb=" N GLU L 10 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL L 115 " --> pdb=" O ARG L 98 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 130 through 134 removed outlier: 6.091A pdb=" N TYR L 186 " --> pdb=" O ASP L 154 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N SER L 187 " --> pdb=" O ALA L 178 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA L 178 " --> pdb=" O SER L 187 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER L 189 " --> pdb=" O PHE L 176 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 160 through 164 921 hydrogen bonds defined for protein. 2346 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: 7.41 Time building geometry restraints manager: 8.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6898 1.35 - 1.47: 5629 1.47 - 1.60: 9205 1.60 - 1.72: 0 1.72 - 1.85: 138 Bond restraints: 21870 Sorted by residual: bond pdb=" C1 MAN U 4 " pdb=" C2 MAN U 4 " ideal model delta sigma weight residual 1.526 1.490 0.036 2.00e-02 2.50e+03 3.30e+00 bond pdb=" C1 MAN O 4 " pdb=" C2 MAN O 4 " ideal model delta sigma weight residual 1.526 1.490 0.036 2.00e-02 2.50e+03 3.26e+00 bond pdb=" C1 MAN R 4 " pdb=" C2 MAN R 4 " ideal model delta sigma weight residual 1.526 1.490 0.036 2.00e-02 2.50e+03 3.19e+00 bond pdb=" C1 BMA U 3 " pdb=" C2 BMA U 3 " ideal model delta sigma weight residual 1.519 1.554 -0.035 2.00e-02 2.50e+03 3.12e+00 bond pdb=" C1 BMA R 3 " pdb=" C2 BMA R 3 " ideal model delta sigma weight residual 1.519 1.553 -0.034 2.00e-02 2.50e+03 2.90e+00 ... (remaining 21865 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 28328 1.72 - 3.44: 1141 3.44 - 5.16: 166 5.16 - 6.87: 55 6.87 - 8.59: 10 Bond angle restraints: 29700 Sorted by residual: angle pdb=" CA VAL J 194 " pdb=" C VAL J 194 " pdb=" N PRO J 195 " ideal model delta sigma weight residual 116.57 120.04 -3.47 9.80e-01 1.04e+00 1.26e+01 angle pdb=" CA VAL L 194 " pdb=" C VAL L 194 " pdb=" N PRO L 195 " ideal model delta sigma weight residual 116.57 120.01 -3.44 9.80e-01 1.04e+00 1.23e+01 angle pdb=" CA VAL H 194 " pdb=" C VAL H 194 " pdb=" N PRO H 195 " ideal model delta sigma weight residual 116.57 119.98 -3.41 9.80e-01 1.04e+00 1.21e+01 angle pdb=" C VAL J 194 " pdb=" CA VAL J 194 " pdb=" CB VAL J 194 " ideal model delta sigma weight residual 109.33 112.39 -3.06 9.80e-01 1.04e+00 9.78e+00 angle pdb=" C VAL H 194 " pdb=" CA VAL H 194 " pdb=" CB VAL H 194 " ideal model delta sigma weight residual 109.33 112.38 -3.05 9.80e-01 1.04e+00 9.68e+00 ... (remaining 29695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.98: 12868 21.98 - 43.97: 734 43.97 - 65.95: 102 65.95 - 87.93: 48 87.93 - 109.91: 24 Dihedral angle restraints: 13776 sinusoidal: 6069 harmonic: 7707 Sorted by residual: dihedral pdb=" CB CYS I 139 " pdb=" SG CYS I 139 " pdb=" SG CYS I 199 " pdb=" CB CYS I 199 " ideal model delta sinusoidal sigma weight residual 93.00 42.08 50.92 1 1.00e+01 1.00e-02 3.55e+01 dihedral pdb=" CB CYS G 139 " pdb=" SG CYS G 139 " pdb=" SG CYS G 199 " pdb=" CB CYS G 199 " ideal model delta sinusoidal sigma weight residual 93.00 47.87 45.13 1 1.00e+01 1.00e-02 2.83e+01 dihedral pdb=" CA CYS E 14 " pdb=" CB CYS E 14 " pdb=" SG CYS E 14 " pdb=" SG CYS F 137 " ideal model delta sinusoidal sigma weight residual -73.00 -0.71 -72.29 1 2.00e+01 2.50e-03 1.67e+01 ... (remaining 13773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3051 0.079 - 0.159: 394 0.159 - 0.238: 23 0.238 - 0.317: 15 0.317 - 0.397: 3 Chirality restraints: 3486 Sorted by residual: chirality pdb=" C3 MAN O 4 " pdb=" C2 MAN O 4 " pdb=" C4 MAN O 4 " pdb=" O3 MAN O 4 " both_signs ideal model delta sigma weight residual False 2.47 2.07 0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" C3 MAN U 4 " pdb=" C2 MAN U 4 " pdb=" C4 MAN U 4 " pdb=" O3 MAN U 4 " both_signs ideal model delta sigma weight residual False 2.47 2.08 0.39 2.00e-01 2.50e+01 3.89e+00 chirality pdb=" C3 MAN R 4 " pdb=" C2 MAN R 4 " pdb=" C4 MAN R 4 " pdb=" O3 MAN R 4 " both_signs ideal model delta sigma weight residual False 2.47 2.08 0.39 2.00e-01 2.50e+01 3.82e+00 ... (remaining 3483 not shown) Planarity restraints: 3771 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 178 " -0.006 2.00e-02 2.50e+03 1.40e-02 3.90e+00 pdb=" CG TYR I 178 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR I 178 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR I 178 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR I 178 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR I 178 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR I 178 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR I 178 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 220 " 0.025 5.00e-02 4.00e+02 3.84e-02 2.35e+00 pdb=" N PRO A 221 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 221 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 221 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 220 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO C 221 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 221 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 221 " -0.021 5.00e-02 4.00e+02 ... (remaining 3768 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 316 2.62 - 3.19: 18968 3.19 - 3.76: 33629 3.76 - 4.33: 48357 4.33 - 4.90: 78252 Nonbonded interactions: 179522 Sorted by model distance: nonbonded pdb=" OE1 GLN G 129 " pdb=" OG SER G 136 " model vdw 2.053 3.040 nonbonded pdb=" ND2 ASN K 163 " pdb=" O THR K 185 " model vdw 2.124 3.120 nonbonded pdb=" O GLY K 24 " pdb=" OG1 THR K 71 " model vdw 2.128 3.040 nonbonded pdb=" OE1 GLN C 210 " pdb=" NE ARG E 220 " model vdw 2.145 3.120 nonbonded pdb=" O TYR I 191 " pdb=" OH TYR I 197 " model vdw 2.164 3.040 ... (remaining 179517 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = (chain 'G' and (resid 2 through 113 or resid 115 through 169 or resid 171 throug \ h 217)) selection = (chain 'I' and (resid 2 through 113 or resid 115 through 169 or resid 171 throug \ h 217)) selection = (chain 'K' and (resid 2 through 113 or resid 115 through 169 or resid 171 throug \ h 217)) } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'P' selection = chain 'S' } ncs_group { reference = chain 'N' selection = chain 'Q' selection = chain 'T' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 56.330 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.130 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: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 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 : 0.005 0.293 21954 Z= 0.243 Angle : 0.860 18.087 29922 Z= 0.432 Chirality : 0.054 0.397 3486 Planarity : 0.005 0.038 3753 Dihedral : 14.882 109.914 8754 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.17 % Allowed : 0.60 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.16), residues: 2649 helix: 1.75 (0.26), residues: 384 sheet: -0.20 (0.17), residues: 867 loop : -1.17 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 50 HIS 0.006 0.001 HIS F 159 PHE 0.019 0.002 PHE I 123 TYR 0.030 0.002 TYR I 178 ARG 0.008 0.001 ARG G 17 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 18) link_NAG-ASN : angle 3.24360 ( 54) link_ALPHA1-6 : bond 0.00952 ( 9) link_ALPHA1-6 : angle 4.11344 ( 27) link_BETA1-4 : bond 0.00497 ( 15) link_BETA1-4 : angle 2.09966 ( 45) link_ALPHA1-2 : bond 0.01334 ( 3) link_ALPHA1-2 : angle 2.44007 ( 9) link_ALPHA1-3 : bond 0.00849 ( 9) link_ALPHA1-3 : angle 4.32139 ( 27) hydrogen bonds : bond 0.15341 ( 879) hydrogen bonds : angle 7.11670 ( 2346) SS BOND : bond 0.06712 ( 30) SS BOND : angle 2.86381 ( 60) covalent geometry : bond 0.00430 (21870) covalent geometry : angle 0.81782 (29700) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 498 time to evaluate : 2.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.7617 (mmm) cc_final: 0.5942 (mmt) REVERT: A 233 TYR cc_start: 0.7243 (m-80) cc_final: 0.7014 (m-10) REVERT: B 73 VAL cc_start: 0.9090 (t) cc_final: 0.8761 (t) REVERT: B 80 LEU cc_start: 0.9427 (tp) cc_final: 0.8812 (tt) REVERT: B 161 VAL cc_start: 0.8221 (m) cc_final: 0.7689 (p) REVERT: C 316 LEU cc_start: 0.7963 (tp) cc_final: 0.7724 (tt) REVERT: D 81 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7568 (mt-10) REVERT: D 89 ILE cc_start: 0.9117 (mt) cc_final: 0.7105 (mt) REVERT: D 94 TYR cc_start: 0.7837 (t80) cc_final: 0.7505 (t80) REVERT: D 95 ASN cc_start: 0.8553 (m-40) cc_final: 0.8238 (m110) REVERT: F 80 LEU cc_start: 0.9427 (tp) cc_final: 0.9205 (tp) REVERT: F 171 PHE cc_start: 0.6141 (m-10) cc_final: 0.5919 (m-10) REVERT: G 143 ASN cc_start: 0.8240 (m110) cc_final: 0.7745 (p0) REVERT: G 159 LEU cc_start: 0.7708 (tp) cc_final: 0.7459 (tt) REVERT: H 121 MET cc_start: 0.8576 (tpt) cc_final: 0.8107 (tpt) REVERT: I 191 TYR cc_start: 0.7706 (t80) cc_final: 0.7425 (t80) REVERT: J 98 ARG cc_start: 0.8142 (ttp-170) cc_final: 0.7869 (ttp-170) REVERT: J 164 TRP cc_start: 0.6005 (m100) cc_final: 0.5792 (m100) REVERT: K 143 ASN cc_start: 0.8374 (m-40) cc_final: 0.7534 (p0) REVERT: K 174 LYS cc_start: 0.7940 (pttt) cc_final: 0.7654 (tptp) outliers start: 4 outliers final: 0 residues processed: 502 average time/residue: 0.4592 time to fit residues: 324.3361 Evaluate side-chains 210 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 3.9990 chunk 200 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 68 optimal weight: 0.0030 chunk 134 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 206 optimal weight: 8.9990 chunk 80 optimal weight: 30.0000 chunk 125 optimal weight: 20.0000 chunk 154 optimal weight: 7.9990 chunk 239 optimal weight: 7.9990 overall best weight: 4.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN B 106 HIS ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 HIS ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** G 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 GLN G 143 ASN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 GLN ** I 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 GLN ** I 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 GLN ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.046381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.035806 restraints weight = 186726.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.036754 restraints weight = 112373.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.037392 restraints weight = 79696.450| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 21954 Z= 0.393 Angle : 0.907 10.631 29922 Z= 0.448 Chirality : 0.051 0.298 3486 Planarity : 0.006 0.069 3753 Dihedral : 11.003 80.902 3960 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.17 % Allowed : 4.47 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.74 (0.16), residues: 2649 helix: 1.50 (0.24), residues: 378 sheet: -0.11 (0.17), residues: 819 loop : -1.29 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP E 84 HIS 0.012 0.003 HIS A 18 PHE 0.026 0.003 PHE I 123 TYR 0.023 0.003 TYR H 111 ARG 0.012 0.001 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00723 ( 18) link_NAG-ASN : angle 2.92600 ( 54) link_ALPHA1-6 : bond 0.01555 ( 9) link_ALPHA1-6 : angle 3.85102 ( 27) link_BETA1-4 : bond 0.00534 ( 15) link_BETA1-4 : angle 2.44723 ( 45) link_ALPHA1-2 : bond 0.00953 ( 3) link_ALPHA1-2 : angle 1.22541 ( 9) link_ALPHA1-3 : bond 0.00962 ( 9) link_ALPHA1-3 : angle 3.07921 ( 27) hydrogen bonds : bond 0.04564 ( 879) hydrogen bonds : angle 6.42679 ( 2346) SS BOND : bond 0.00549 ( 30) SS BOND : angle 1.25909 ( 60) covalent geometry : bond 0.00825 (21870) covalent geometry : angle 0.88259 (29700) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 252 time to evaluate : 2.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 HIS cc_start: 0.7996 (p90) cc_final: 0.7773 (p-80) REVERT: A 123 GLU cc_start: 0.8054 (tt0) cc_final: 0.7498 (tt0) REVERT: B 17 MET cc_start: 0.3885 (ttm) cc_final: 0.3271 (ttp) REVERT: B 103 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8705 (tp30) REVERT: B 133 MET cc_start: 0.7105 (mtm) cc_final: 0.5852 (mmm) REVERT: B 170 ARG cc_start: 0.8647 (ttt180) cc_final: 0.8154 (ttm110) REVERT: D 83 TYR cc_start: 0.8899 (t80) cc_final: 0.8677 (t80) REVERT: E 18 HIS cc_start: 0.8438 (p-80) cc_final: 0.8189 (p-80) REVERT: E 27 LYS cc_start: 0.8542 (ptmm) cc_final: 0.8008 (mptt) REVERT: E 32 ASP cc_start: 0.8909 (m-30) cc_final: 0.8531 (p0) REVERT: E 190 GLU cc_start: 0.9253 (tt0) cc_final: 0.8996 (tt0) REVERT: G 143 ASN cc_start: 0.8953 (m-40) cc_final: 0.8135 (p0) REVERT: G 197 TYR cc_start: 0.8536 (m-10) cc_final: 0.7934 (m-80) REVERT: H 10 GLU cc_start: 0.8885 (tp30) cc_final: 0.8567 (tp30) REVERT: H 81 MET cc_start: 0.8542 (tmm) cc_final: 0.8281 (tmm) REVERT: J 81 MET cc_start: 0.8640 (tmm) cc_final: 0.8434 (tmm) REVERT: J 106 MET cc_start: 0.8809 (mtm) cc_final: 0.8437 (mtm) REVERT: J 121 MET cc_start: 0.9319 (tpt) cc_final: 0.8933 (tpt) REVERT: K 143 ASN cc_start: 0.8632 (m-40) cc_final: 0.7533 (p0) REVERT: K 174 LYS cc_start: 0.8234 (pttt) cc_final: 0.7885 (tptp) REVERT: L 81 MET cc_start: 0.8606 (tmm) cc_final: 0.8127 (tmm) REVERT: L 121 MET cc_start: 0.9237 (tpt) cc_final: 0.8762 (tpt) REVERT: L 148 LEU cc_start: 0.7914 (mt) cc_final: 0.7390 (pt) outliers start: 4 outliers final: 1 residues processed: 256 average time/residue: 0.4141 time to fit residues: 154.2630 Evaluate side-chains 173 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 2.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 196 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 chunk 180 optimal weight: 9.9990 chunk 186 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 178 optimal weight: 7.9990 chunk 120 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 231 optimal weight: 0.9980 chunk 182 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS G 6 GLN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 GLN I 39 GLN ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 GLN ** I 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.047419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.036704 restraints weight = 182049.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.037707 restraints weight = 108482.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.038372 restraints weight = 76150.113| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21954 Z= 0.184 Angle : 0.692 9.683 29922 Z= 0.341 Chirality : 0.048 0.302 3486 Planarity : 0.005 0.053 3753 Dihedral : 9.915 74.335 3960 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.60 (0.16), residues: 2649 helix: 1.68 (0.25), residues: 384 sheet: -0.11 (0.17), residues: 864 loop : -1.19 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 153 HIS 0.011 0.001 HIS B 159 PHE 0.017 0.002 PHE A 294 TYR 0.017 0.002 TYR E 105 ARG 0.006 0.001 ARG I 17 Details of bonding type rmsd link_NAG-ASN : bond 0.00553 ( 18) link_NAG-ASN : angle 2.64795 ( 54) link_ALPHA1-6 : bond 0.00618 ( 9) link_ALPHA1-6 : angle 2.94499 ( 27) link_BETA1-4 : bond 0.00313 ( 15) link_BETA1-4 : angle 1.84474 ( 45) link_ALPHA1-2 : bond 0.01249 ( 3) link_ALPHA1-2 : angle 1.30699 ( 9) link_ALPHA1-3 : bond 0.00370 ( 9) link_ALPHA1-3 : angle 2.83346 ( 27) hydrogen bonds : bond 0.03647 ( 879) hydrogen bonds : angle 5.86467 ( 2346) SS BOND : bond 0.00372 ( 30) SS BOND : angle 0.87847 ( 60) covalent geometry : bond 0.00392 (21870) covalent geometry : angle 0.66834 (29700) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 2.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 PHE cc_start: 0.8622 (p90) cc_final: 0.8316 (p90) REVERT: B 133 MET cc_start: 0.7357 (mtm) cc_final: 0.5483 (ttp) REVERT: B 139 LYS cc_start: 0.8647 (tppt) cc_final: 0.8384 (tppp) REVERT: B 170 ARG cc_start: 0.8644 (ttt180) cc_final: 0.8253 (ttm110) REVERT: C 268 MET cc_start: 0.8313 (ttm) cc_final: 0.8014 (ttm) REVERT: E 27 LYS cc_start: 0.8618 (ptmm) cc_final: 0.8098 (mptt) REVERT: E 190 GLU cc_start: 0.9256 (tt0) cc_final: 0.9034 (tt0) REVERT: F 105 GLN cc_start: 0.8592 (pp30) cc_final: 0.8200 (pp30) REVERT: G 143 ASN cc_start: 0.8749 (m-40) cc_final: 0.7896 (p0) REVERT: G 148 GLU cc_start: 0.8414 (pm20) cc_final: 0.8121 (pm20) REVERT: G 197 TYR cc_start: 0.8511 (m-10) cc_final: 0.8006 (m-80) REVERT: H 10 GLU cc_start: 0.8863 (tp30) cc_final: 0.8543 (tp30) REVERT: H 81 MET cc_start: 0.8602 (tmm) cc_final: 0.8325 (tmm) REVERT: I 143 ASN cc_start: 0.8503 (m-40) cc_final: 0.7267 (p0) REVERT: I 191 TYR cc_start: 0.8092 (t80) cc_final: 0.7567 (t80) REVERT: J 81 MET cc_start: 0.8685 (tmm) cc_final: 0.8473 (tmm) REVERT: J 106 MET cc_start: 0.8813 (mtm) cc_final: 0.8523 (mtm) REVERT: J 121 MET cc_start: 0.9272 (tpt) cc_final: 0.8924 (tpt) REVERT: J 164 TRP cc_start: 0.6694 (m100) cc_final: 0.6103 (m100) REVERT: J 218 ASP cc_start: 0.7876 (m-30) cc_final: 0.7012 (m-30) REVERT: K 143 ASN cc_start: 0.8655 (m-40) cc_final: 0.7540 (p0) REVERT: K 174 LYS cc_start: 0.8228 (pttt) cc_final: 0.7779 (tptp) REVERT: L 10 GLU cc_start: 0.8770 (tp30) cc_final: 0.8401 (tm-30) REVERT: L 81 MET cc_start: 0.8675 (tmm) cc_final: 0.8239 (tmm) REVERT: L 121 MET cc_start: 0.9206 (tpt) cc_final: 0.8703 (tpt) REVERT: L 148 LEU cc_start: 0.7880 (mt) cc_final: 0.7406 (pt) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.4269 time to fit residues: 163.9193 Evaluate side-chains 175 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 217 optimal weight: 5.9990 chunk 255 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 144 optimal weight: 0.0870 chunk 173 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 209 optimal weight: 9.9990 chunk 131 optimal weight: 0.8980 chunk 175 optimal weight: 0.9990 chunk 235 optimal weight: 5.9990 chunk 92 optimal weight: 0.4980 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN ** I 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 57 GLN ** K 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 157 ASN ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 207 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.048165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.037468 restraints weight = 181734.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.038496 restraints weight = 107592.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.039184 restraints weight = 75124.867| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21954 Z= 0.125 Angle : 0.644 9.692 29922 Z= 0.317 Chirality : 0.047 0.307 3486 Planarity : 0.005 0.075 3753 Dihedral : 8.889 68.300 3960 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.09 % Allowed : 3.18 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.50 (0.16), residues: 2649 helix: 1.47 (0.25), residues: 402 sheet: 0.05 (0.18), residues: 825 loop : -1.11 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 47 HIS 0.009 0.001 HIS F 159 PHE 0.026 0.001 PHE B 171 TYR 0.023 0.002 TYR E 257 ARG 0.011 0.001 ARG B 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00537 ( 18) link_NAG-ASN : angle 2.45112 ( 54) link_ALPHA1-6 : bond 0.00419 ( 9) link_ALPHA1-6 : angle 2.46935 ( 27) link_BETA1-4 : bond 0.00291 ( 15) link_BETA1-4 : angle 1.68303 ( 45) link_ALPHA1-2 : bond 0.00825 ( 3) link_ALPHA1-2 : angle 1.37122 ( 9) link_ALPHA1-3 : bond 0.00577 ( 9) link_ALPHA1-3 : angle 2.90925 ( 27) hydrogen bonds : bond 0.03395 ( 879) hydrogen bonds : angle 5.52230 ( 2346) SS BOND : bond 0.00292 ( 30) SS BOND : angle 0.81468 ( 60) covalent geometry : bond 0.00272 (21870) covalent geometry : angle 0.62283 (29700) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 259 time to evaluate : 2.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 HIS cc_start: 0.8016 (p-80) cc_final: 0.7701 (p-80) REVERT: B 9 PHE cc_start: 0.8552 (p90) cc_final: 0.8258 (p90) REVERT: B 76 ARG cc_start: 0.8205 (ttt-90) cc_final: 0.7699 (ttt-90) REVERT: B 82 LYS cc_start: 0.9419 (mmmm) cc_final: 0.9201 (mtmm) REVERT: B 100 VAL cc_start: 0.9706 (t) cc_final: 0.9452 (t) REVERT: B 170 ARG cc_start: 0.8640 (ttt180) cc_final: 0.8378 (ttm170) REVERT: D 83 TYR cc_start: 0.8882 (t80) cc_final: 0.8655 (t80) REVERT: E 18 HIS cc_start: 0.8496 (p-80) cc_final: 0.7051 (p-80) REVERT: E 27 LYS cc_start: 0.8670 (ptmm) cc_final: 0.8154 (mptt) REVERT: E 33 GLN cc_start: 0.8249 (mm-40) cc_final: 0.8036 (tp-100) REVERT: E 190 GLU cc_start: 0.9267 (tt0) cc_final: 0.8997 (tt0) REVERT: F 17 MET cc_start: 0.2622 (mtm) cc_final: 0.2176 (mtm) REVERT: F 21 TRP cc_start: 0.9280 (m100) cc_final: 0.8710 (m100) REVERT: F 170 ARG cc_start: 0.7883 (ptp-110) cc_final: 0.7099 (ptp-110) REVERT: G 49 LEU cc_start: 0.9128 (pp) cc_final: 0.8908 (mt) REVERT: G 143 ASN cc_start: 0.8621 (m-40) cc_final: 0.7838 (p0) REVERT: G 148 GLU cc_start: 0.8455 (pm20) cc_final: 0.7982 (pm20) REVERT: G 191 TYR cc_start: 0.8743 (t80) cc_final: 0.8419 (t80) REVERT: G 197 TYR cc_start: 0.8403 (m-10) cc_final: 0.7951 (m-80) REVERT: H 81 MET cc_start: 0.8520 (tmm) cc_final: 0.8300 (tmm) REVERT: H 106 MET cc_start: 0.8511 (mtm) cc_final: 0.8304 (mtm) REVERT: H 121 MET cc_start: 0.9016 (tpt) cc_final: 0.8446 (tpt) REVERT: I 191 TYR cc_start: 0.8107 (t80) cc_final: 0.7589 (t80) REVERT: J 81 MET cc_start: 0.8491 (tmm) cc_final: 0.8146 (tmm) REVERT: J 98 ARG cc_start: 0.8702 (ttp-170) cc_final: 0.8130 (ttp-170) REVERT: J 106 MET cc_start: 0.8869 (mtm) cc_final: 0.8573 (mtm) REVERT: J 121 MET cc_start: 0.9240 (tpt) cc_final: 0.8875 (tpt) REVERT: J 154 ASP cc_start: 0.7635 (p0) cc_final: 0.7374 (p0) REVERT: J 164 TRP cc_start: 0.6451 (m100) cc_final: 0.5911 (m100) REVERT: J 218 ASP cc_start: 0.8118 (m-30) cc_final: 0.7423 (m-30) REVERT: K 36 HIS cc_start: 0.6711 (m-70) cc_final: 0.6363 (m170) REVERT: K 174 LYS cc_start: 0.8169 (pttt) cc_final: 0.7765 (tptp) REVERT: L 10 GLU cc_start: 0.8666 (tp30) cc_final: 0.8402 (tm-30) REVERT: L 81 MET cc_start: 0.8601 (tmm) cc_final: 0.8337 (tmm) REVERT: L 121 MET cc_start: 0.9163 (tpt) cc_final: 0.8638 (tpt) outliers start: 2 outliers final: 0 residues processed: 260 average time/residue: 0.4496 time to fit residues: 169.7610 Evaluate side-chains 165 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 2.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 88 optimal weight: 4.9990 chunk 182 optimal weight: 0.4980 chunk 148 optimal weight: 10.0000 chunk 222 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 140 optimal weight: 20.0000 chunk 86 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 232 optimal weight: 10.0000 chunk 259 optimal weight: 5.9990 chunk 197 optimal weight: 8.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 HIS ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN G 6 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 143 ASN ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 207 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.046747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.036274 restraints weight = 189185.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.037232 restraints weight = 113133.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.037882 restraints weight = 80140.094| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 21954 Z= 0.212 Angle : 0.702 10.997 29922 Z= 0.347 Chirality : 0.047 0.302 3486 Planarity : 0.005 0.047 3753 Dihedral : 8.399 62.960 3960 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.04 % Allowed : 2.36 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.52 (0.16), residues: 2649 helix: 1.12 (0.25), residues: 402 sheet: -0.02 (0.18), residues: 822 loop : -0.96 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 37 HIS 0.005 0.001 HIS G 194 PHE 0.023 0.002 PHE L 176 TYR 0.023 0.002 TYR E 233 ARG 0.009 0.001 ARG K 216 Details of bonding type rmsd link_NAG-ASN : bond 0.00837 ( 18) link_NAG-ASN : angle 2.56762 ( 54) link_ALPHA1-6 : bond 0.00493 ( 9) link_ALPHA1-6 : angle 2.87303 ( 27) link_BETA1-4 : bond 0.00316 ( 15) link_BETA1-4 : angle 1.67587 ( 45) link_ALPHA1-2 : bond 0.01073 ( 3) link_ALPHA1-2 : angle 1.15154 ( 9) link_ALPHA1-3 : bond 0.00465 ( 9) link_ALPHA1-3 : angle 2.85755 ( 27) hydrogen bonds : bond 0.03639 ( 879) hydrogen bonds : angle 5.67560 ( 2346) SS BOND : bond 0.00491 ( 30) SS BOND : angle 0.96527 ( 60) covalent geometry : bond 0.00453 (21870) covalent geometry : angle 0.68084 (29700) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 215 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 HIS cc_start: 0.8129 (p-80) cc_final: 0.7907 (p-80) REVERT: A 27 LYS cc_start: 0.8726 (pptt) cc_final: 0.7993 (mptt) REVERT: A 311 GLN cc_start: 0.9329 (OUTLIER) cc_final: 0.9059 (mp10) REVERT: B 9 PHE cc_start: 0.8595 (p90) cc_final: 0.8284 (p90) REVERT: B 170 ARG cc_start: 0.8653 (ttt180) cc_final: 0.8316 (ttm110) REVERT: D 42 GLN cc_start: 0.9085 (pm20) cc_final: 0.8781 (pm20) REVERT: E 27 LYS cc_start: 0.8717 (ptmm) cc_final: 0.8511 (ptmm) REVERT: E 168 MET cc_start: 0.8667 (mmt) cc_final: 0.8430 (mmt) REVERT: E 190 GLU cc_start: 0.9293 (tt0) cc_final: 0.8998 (tt0) REVERT: F 17 MET cc_start: 0.2686 (mtm) cc_final: 0.1992 (mtm) REVERT: G 143 ASN cc_start: 0.8574 (m-40) cc_final: 0.7750 (p0) REVERT: G 148 GLU cc_start: 0.8651 (pm20) cc_final: 0.8418 (pm20) REVERT: G 197 TYR cc_start: 0.8547 (m-10) cc_final: 0.7905 (m-80) REVERT: H 81 MET cc_start: 0.8654 (tmm) cc_final: 0.8445 (tmm) REVERT: H 218 ASP cc_start: 0.8599 (m-30) cc_final: 0.8023 (m-30) REVERT: I 191 TYR cc_start: 0.8073 (t80) cc_final: 0.7603 (t80) REVERT: J 81 MET cc_start: 0.8669 (tmm) cc_final: 0.8312 (tmm) REVERT: J 106 MET cc_start: 0.8986 (mtm) cc_final: 0.8734 (mtm) REVERT: J 121 MET cc_start: 0.9290 (tpt) cc_final: 0.8833 (tpt) REVERT: J 218 ASP cc_start: 0.8283 (m-30) cc_final: 0.7516 (m-30) REVERT: K 174 LYS cc_start: 0.8194 (pttt) cc_final: 0.7781 (tptp) REVERT: L 10 GLU cc_start: 0.8702 (tp30) cc_final: 0.8352 (tm-30) REVERT: L 81 MET cc_start: 0.8527 (tmm) cc_final: 0.8230 (tmm) REVERT: L 121 MET cc_start: 0.9170 (tpt) cc_final: 0.8592 (tpt) outliers start: 1 outliers final: 0 residues processed: 216 average time/residue: 0.3991 time to fit residues: 127.2071 Evaluate side-chains 156 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 137 optimal weight: 30.0000 chunk 230 optimal weight: 7.9990 chunk 225 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 chunk 260 optimal weight: 4.9990 chunk 249 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 HIS ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 152 GLN ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 GLN L 209 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.045441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.035041 restraints weight = 189790.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.035968 restraints weight = 114050.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.036576 restraints weight = 80771.110| |-----------------------------------------------------------------------------| r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 21954 Z= 0.326 Angle : 0.824 11.219 29922 Z= 0.407 Chirality : 0.049 0.288 3486 Planarity : 0.006 0.068 3753 Dihedral : 8.617 58.664 3960 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.04 % Allowed : 2.41 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.88 (0.16), residues: 2649 helix: 0.63 (0.25), residues: 402 sheet: -0.17 (0.18), residues: 804 loop : -1.17 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 37 HIS 0.007 0.002 HIS C 183 PHE 0.027 0.003 PHE L 132 TYR 0.025 0.003 TYR E 257 ARG 0.014 0.001 ARG F 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00784 ( 18) link_NAG-ASN : angle 2.76977 ( 54) link_ALPHA1-6 : bond 0.00756 ( 9) link_ALPHA1-6 : angle 3.42905 ( 27) link_BETA1-4 : bond 0.00442 ( 15) link_BETA1-4 : angle 1.73332 ( 45) link_ALPHA1-2 : bond 0.01338 ( 3) link_ALPHA1-2 : angle 1.18218 ( 9) link_ALPHA1-3 : bond 0.00278 ( 9) link_ALPHA1-3 : angle 2.92952 ( 27) hydrogen bonds : bond 0.04066 ( 879) hydrogen bonds : angle 6.12176 ( 2346) SS BOND : bond 0.00643 ( 30) SS BOND : angle 1.31108 ( 60) covalent geometry : bond 0.00690 (21870) covalent geometry : angle 0.80205 (29700) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 2.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8589 (pptt) cc_final: 0.8097 (mptt) REVERT: E 27 LYS cc_start: 0.8764 (ptmm) cc_final: 0.8481 (mmtp) REVERT: E 168 MET cc_start: 0.8523 (mmt) cc_final: 0.8322 (mmt) REVERT: F 17 MET cc_start: 0.2750 (mtm) cc_final: 0.2287 (mtm) REVERT: F 76 ARG cc_start: 0.8291 (ttt180) cc_final: 0.8083 (ttt90) REVERT: G 143 ASN cc_start: 0.8566 (m-40) cc_final: 0.7379 (p0) REVERT: G 191 TYR cc_start: 0.8777 (t80) cc_final: 0.8433 (t80) REVERT: G 197 TYR cc_start: 0.8621 (m-10) cc_final: 0.8012 (m-80) REVERT: H 81 MET cc_start: 0.8645 (tmm) cc_final: 0.8422 (tmm) REVERT: I 191 TYR cc_start: 0.8039 (t80) cc_final: 0.7726 (t80) REVERT: J 81 MET cc_start: 0.8636 (tmm) cc_final: 0.8240 (tmm) REVERT: J 121 MET cc_start: 0.9274 (tpt) cc_final: 0.8929 (tpt) REVERT: K 174 LYS cc_start: 0.8250 (pttt) cc_final: 0.7857 (tptp) REVERT: K 191 TYR cc_start: 0.8534 (t80) cc_final: 0.8272 (t80) REVERT: L 10 GLU cc_start: 0.8521 (tp30) cc_final: 0.7982 (tm-30) REVERT: L 81 MET cc_start: 0.8659 (tmm) cc_final: 0.8297 (tmm) outliers start: 1 outliers final: 1 residues processed: 193 average time/residue: 0.4227 time to fit residues: 121.4550 Evaluate side-chains 137 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 0.0470 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 188 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 overall best weight: 0.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 152 GLN ** I 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.046760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.036397 restraints weight = 184898.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.037361 restraints weight = 110469.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.038000 restraints weight = 77939.379| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21954 Z= 0.134 Angle : 0.676 11.752 29922 Z= 0.331 Chirality : 0.048 0.296 3486 Planarity : 0.005 0.058 3753 Dihedral : 8.063 60.751 3960 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.16), residues: 2649 helix: 1.21 (0.25), residues: 399 sheet: -0.15 (0.17), residues: 870 loop : -1.05 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 222 HIS 0.007 0.001 HIS K 36 PHE 0.021 0.002 PHE L 176 TYR 0.038 0.002 TYR H 32 ARG 0.005 0.001 ARG B 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00564 ( 18) link_NAG-ASN : angle 2.52187 ( 54) link_ALPHA1-6 : bond 0.00484 ( 9) link_ALPHA1-6 : angle 2.48121 ( 27) link_BETA1-4 : bond 0.00281 ( 15) link_BETA1-4 : angle 1.47973 ( 45) link_ALPHA1-2 : bond 0.00983 ( 3) link_ALPHA1-2 : angle 1.45227 ( 9) link_ALPHA1-3 : bond 0.00570 ( 9) link_ALPHA1-3 : angle 2.94783 ( 27) hydrogen bonds : bond 0.03506 ( 879) hydrogen bonds : angle 5.72095 ( 2346) SS BOND : bond 0.00349 ( 30) SS BOND : angle 0.91959 ( 60) covalent geometry : bond 0.00288 (21870) covalent geometry : angle 0.65503 (29700) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 2.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8550 (pptt) cc_final: 0.8145 (mptt) REVERT: E 27 LYS cc_start: 0.8766 (ptmm) cc_final: 0.8487 (ptmm) REVERT: E 190 GLU cc_start: 0.9290 (tt0) cc_final: 0.8990 (tt0) REVERT: F 17 MET cc_start: 0.2163 (mtm) cc_final: 0.1705 (mtm) REVERT: G 36 HIS cc_start: 0.7177 (m-70) cc_final: 0.6953 (m170) REVERT: G 143 ASN cc_start: 0.8428 (m-40) cc_final: 0.7330 (p0) REVERT: G 191 TYR cc_start: 0.8787 (t80) cc_final: 0.8297 (t80) REVERT: G 197 TYR cc_start: 0.8405 (m-10) cc_final: 0.7819 (m-80) REVERT: H 121 MET cc_start: 0.9082 (tpt) cc_final: 0.8471 (tpt) REVERT: I 191 TYR cc_start: 0.8014 (t80) cc_final: 0.7562 (t80) REVERT: J 81 MET cc_start: 0.8358 (tmm) cc_final: 0.8085 (tmm) REVERT: J 106 MET cc_start: 0.8875 (mtm) cc_final: 0.8609 (ttm) REVERT: J 121 MET cc_start: 0.9254 (tpt) cc_final: 0.8908 (tpt) REVERT: K 174 LYS cc_start: 0.8220 (pttt) cc_final: 0.7841 (tptp) REVERT: L 81 MET cc_start: 0.8548 (tmm) cc_final: 0.8344 (tmm) REVERT: L 121 MET cc_start: 0.8927 (tpp) cc_final: 0.8365 (tpt) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.5320 time to fit residues: 168.3825 Evaluate side-chains 148 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 3.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 27 optimal weight: 0.1980 chunk 182 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 243 optimal weight: 8.9990 chunk 151 optimal weight: 8.9990 chunk 216 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 143 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.045669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.035351 restraints weight = 192125.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.036295 restraints weight = 114351.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.036916 restraints weight = 80648.144| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 21954 Z= 0.219 Angle : 0.721 11.971 29922 Z= 0.354 Chirality : 0.048 0.293 3486 Planarity : 0.005 0.062 3753 Dihedral : 8.144 62.013 3960 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.70 (0.16), residues: 2649 helix: 1.01 (0.25), residues: 399 sheet: -0.12 (0.18), residues: 822 loop : -1.10 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 222 HIS 0.006 0.001 HIS K 36 PHE 0.028 0.002 PHE L 176 TYR 0.024 0.002 TYR H 32 ARG 0.021 0.001 ARG F 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00627 ( 18) link_NAG-ASN : angle 2.62222 ( 54) link_ALPHA1-6 : bond 0.00529 ( 9) link_ALPHA1-6 : angle 2.92256 ( 27) link_BETA1-4 : bond 0.00319 ( 15) link_BETA1-4 : angle 1.57641 ( 45) link_ALPHA1-2 : bond 0.01064 ( 3) link_ALPHA1-2 : angle 1.25560 ( 9) link_ALPHA1-3 : bond 0.00402 ( 9) link_ALPHA1-3 : angle 2.80172 ( 27) hydrogen bonds : bond 0.03658 ( 879) hydrogen bonds : angle 5.81293 ( 2346) SS BOND : bond 0.00440 ( 30) SS BOND : angle 1.16348 ( 60) covalent geometry : bond 0.00469 (21870) covalent geometry : angle 0.69971 (29700) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 2.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8609 (pptt) cc_final: 0.8163 (mptt) REVERT: F 17 MET cc_start: 0.2471 (mtm) cc_final: 0.2027 (mtm) REVERT: F 133 MET cc_start: 0.6448 (mmm) cc_final: 0.5853 (mpp) REVERT: G 143 ASN cc_start: 0.8525 (m-40) cc_final: 0.7410 (p0) REVERT: G 191 TYR cc_start: 0.8859 (t80) cc_final: 0.8427 (t80) REVERT: G 197 TYR cc_start: 0.8581 (m-10) cc_final: 0.7706 (m-80) REVERT: H 121 MET cc_start: 0.9113 (tpt) cc_final: 0.8431 (tpt) REVERT: I 191 TYR cc_start: 0.8058 (t80) cc_final: 0.7614 (t80) REVERT: J 81 MET cc_start: 0.8500 (tmm) cc_final: 0.8265 (tmm) REVERT: J 121 MET cc_start: 0.9266 (tpt) cc_final: 0.8918 (tpt) REVERT: K 174 LYS cc_start: 0.8252 (pttt) cc_final: 0.7818 (tptp) REVERT: L 81 MET cc_start: 0.8632 (tmm) cc_final: 0.8401 (tmm) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.4006 time to fit residues: 112.3386 Evaluate side-chains 140 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 57.4602 > 50: distance: 13 - 21: 3.866 distance: 21 - 22: 7.245 distance: 22 - 23: 5.277 distance: 22 - 25: 6.473 distance: 23 - 24: 33.303 distance: 23 - 29: 24.306 distance: 25 - 26: 10.422 distance: 25 - 27: 12.221 distance: 26 - 28: 16.319 distance: 29 - 30: 13.172 distance: 29 - 161: 24.832 distance: 30 - 31: 16.575 distance: 30 - 33: 6.588 distance: 31 - 32: 5.165 distance: 31 - 37: 3.863 distance: 32 - 176: 8.889 distance: 33 - 34: 13.931 distance: 34 - 35: 20.412 distance: 34 - 36: 13.062 distance: 38 - 39: 4.818 distance: 39 - 40: 7.627 distance: 41 - 42: 3.791 distance: 42 - 43: 6.367 distance: 42 - 44: 15.658 distance: 45 - 46: 3.434 distance: 45 - 179: 10.670 distance: 46 - 47: 8.344 distance: 47 - 48: 7.111 distance: 47 - 49: 4.808 distance: 49 - 50: 7.918 distance: 50 - 51: 7.405 distance: 50 - 53: 4.753 distance: 51 - 52: 8.411 distance: 51 - 57: 3.153 distance: 53 - 54: 5.387 distance: 53 - 55: 9.325 distance: 54 - 56: 7.610 distance: 58 - 61: 5.243 distance: 59 - 60: 6.929 distance: 59 - 65: 3.384 distance: 61 - 62: 5.725 distance: 62 - 63: 4.511 distance: 62 - 64: 7.631 distance: 65 - 66: 5.798 distance: 66 - 69: 5.861 distance: 67 - 68: 9.449 distance: 67 - 71: 3.754 distance: 69 - 70: 4.064 distance: 73 - 78: 3.487 distance: 74 - 102: 6.272 distance: 75 - 76: 4.901 distance: 75 - 77: 5.146 distance: 78 - 79: 3.092 distance: 79 - 80: 3.591 distance: 79 - 82: 4.454 distance: 80 - 81: 5.269 distance: 80 - 86: 5.617 distance: 81 - 107: 5.798 distance: 82 - 83: 4.425 distance: 83 - 84: 3.255 distance: 83 - 85: 5.234 distance: 86 - 87: 4.342 distance: 87 - 88: 4.527 distance: 88 - 89: 3.117 distance: 90 - 91: 5.976 distance: 90 - 92: 7.016 distance: 91 - 93: 4.869