Starting phenix.real_space_refine on Mon Aug 25 02:48:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j5p_35989/08_2025/8j5p_35989.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j5p_35989/08_2025/8j5p_35989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j5p_35989/08_2025/8j5p_35989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j5p_35989/08_2025/8j5p_35989.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j5p_35989/08_2025/8j5p_35989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j5p_35989/08_2025/8j5p_35989.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 7 Type Number sf(0) Gaussians Fe 5 7.16 5 P 3 5.49 5 Mg 48 5.21 5 S 75 5.16 5 C 16876 2.51 5 N 3316 2.21 5 O 3414 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23737 Number of models: 1 Model: "" Number of chains: 70 Chain: "0" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "1" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "2" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "3" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "4" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "5" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "6" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "7" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "8" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "9" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "A" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "B" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "C" Number of atoms: 2404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2404 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 24, 'TRANS': 290} Chain: "D" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "E" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "F" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "H" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "I" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "J" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "K" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "L" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2375 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 16, 'TRANS': 283} Chain breaks: 1 Chain: "M" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2488 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 16, 'TRANS': 289} Chain: "N" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "O" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "P" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "Q" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "R" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "S" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "T" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "U" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "V" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "W" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "X" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 206 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "Y" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 259 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "Z" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 362 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 4, 'TRANS': 42} Chain: "0" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "1" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "5" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 148 Unusual residues: {'BCL': 1, 'KGD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "7" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "9" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 254 Unusual residues: {'HEM': 4, 'KGD': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 148 Unusual residues: {'BCL': 1, 'KGD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 214 Unusual residues: {'BCL': 2, 'KGD': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 407 Unusual residues: {'BCL': 2, 'BPB': 2, 'MQE': 1, 'PGV': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 224 Unusual residues: {' FE': 1, 'BCL': 1, 'BPB': 1, 'MQE': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'MQE:plan-2': 1, 'MQE:plan-3': 1, 'MQE:plan-4': 1, 'MQE:plan-5': 1, 'MQE:plan-6': 1, 'MQE:plan-9': 1, 'MQE:plan-10': 1, 'MQE:plan-11': 1, 'MQE:plan-12': 1} Unresolved non-hydrogen planarities: 44 Chain: "N" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 183 Unusual residues: {'BCL': 1, 'KGD': 2, 'PGV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.80, per 1000 atoms: 0.20 Number of scatterers: 23737 At special positions: 0 Unit cell: (127.699, 137.522, 138.415, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 5 26.01 S 75 16.00 P 3 15.00 Mg 48 11.99 O 3414 8.00 N 3316 7.00 C 16876 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=60, symmetry=0 Number of additional bonds: simple=60, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 629.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4372 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 4 sheets defined 67.0% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain '0' and resid 20 through 51 removed outlier: 4.534A pdb=" N LEU 0 24 " --> pdb=" O ASN 0 20 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL 0 25 " --> pdb=" O ALA 0 21 " (cutoff:3.500A) Processing helix chain '1' and resid 6 through 34 removed outlier: 3.555A pdb=" N SER 1 11 " --> pdb=" O GLU 1 7 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL 1 14 " --> pdb=" O THR 1 10 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY 1 34 " --> pdb=" O VAL 1 30 " (cutoff:3.500A) Processing helix chain '2' and resid 21 through 51 removed outlier: 3.936A pdb=" N VAL 2 25 " --> pdb=" O ALA 2 21 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 34 removed outlier: 4.143A pdb=" N GLY 3 34 " --> pdb=" O VAL 3 30 " (cutoff:3.500A) Processing helix chain '4' and resid 21 through 51 removed outlier: 4.142A pdb=" N VAL 4 25 " --> pdb=" O ALA 4 21 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 33 Processing helix chain '6' and resid 21 through 51 removed outlier: 3.895A pdb=" N VAL 6 25 " --> pdb=" O ALA 6 21 " (cutoff:3.500A) Processing helix chain '7' and resid 7 through 34 removed outlier: 4.284A pdb=" N GLY 7 34 " --> pdb=" O VAL 7 30 " (cutoff:3.500A) Processing helix chain '8' and resid 21 through 51 removed outlier: 3.844A pdb=" N VAL 8 25 " --> pdb=" O ALA 8 21 " (cutoff:3.500A) Processing helix chain '9' and resid 7 through 33 Processing helix chain 'A' and resid 7 through 34 removed outlier: 4.058A pdb=" N GLY A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 51 removed outlier: 3.668A pdb=" N TRP B 23 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU B 24 " --> pdb=" O ASN B 20 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 14 Processing helix chain 'C' and resid 15 through 47 removed outlier: 3.554A pdb=" N TYR C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE C 22 " --> pdb=" O GLY C 18 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 85 removed outlier: 3.596A pdb=" N ALA C 77 " --> pdb=" O GLU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 109 Processing helix chain 'C' and resid 109 through 115 Processing helix chain 'C' and resid 117 through 121 Processing helix chain 'C' and resid 135 through 156 removed outlier: 3.937A pdb=" N LYS C 139 " --> pdb=" O ASN C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 176 removed outlier: 4.396A pdb=" N CYS C 174 " --> pdb=" O THR C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 237 Processing helix chain 'C' and resid 255 through 274 removed outlier: 4.222A pdb=" N HIS C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 289 removed outlier: 4.390A pdb=" N GLY C 288 " --> pdb=" O ILE C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 297 removed outlier: 4.264A pdb=" N CYS C 296 " --> pdb=" O SER C 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 33 Processing helix chain 'E' and resid 19 through 51 removed outlier: 4.367A pdb=" N LEU E 24 " --> pdb=" O ASN E 20 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL E 25 " --> pdb=" O ALA E 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 33 Processing helix chain 'G' and resid 21 through 51 removed outlier: 3.953A pdb=" N VAL G 25 " --> pdb=" O ALA G 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 34 removed outlier: 4.185A pdb=" N GLY H 34 " --> pdb=" O VAL H 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 51 removed outlier: 3.749A pdb=" N TRP I 23 " --> pdb=" O ASN I 19 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU I 24 " --> pdb=" O ASN I 20 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL I 25 " --> pdb=" O ALA I 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 34 removed outlier: 4.123A pdb=" N GLY J 34 " --> pdb=" O VAL J 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 51 removed outlier: 3.514A pdb=" N TRP K 23 " --> pdb=" O ASN K 19 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU K 24 " --> pdb=" O ASN K 20 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL K 25 " --> pdb=" O ALA K 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 44 removed outlier: 4.395A pdb=" N ILE L 39 " --> pdb=" O PRO L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 55 removed outlier: 3.655A pdb=" N ARG L 53 " --> pdb=" O THR L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 93 removed outlier: 3.742A pdb=" N ALA L 74 " --> pdb=" O GLY L 70 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE L 75 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY L 91 " --> pdb=" O TYR L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 113 Processing helix chain 'L' and resid 122 through 150 removed outlier: 3.703A pdb=" N PHE L 126 " --> pdb=" O GLY L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 154 through 172 removed outlier: 3.623A pdb=" N LEU L 170 " --> pdb=" O SER L 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 179 Processing helix chain 'L' and resid 191 through 203 removed outlier: 3.614A pdb=" N TYR L 203 " --> pdb=" O ILE L 199 " (cutoff:3.500A) Processing helix chain 'L' and resid 205 through 208 Processing helix chain 'L' and resid 209 through 236 removed outlier: 3.818A pdb=" N GLU L 236 " --> pdb=" O ALA L 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 244 through 253 Processing helix chain 'L' and resid 261 through 288 removed outlier: 3.647A pdb=" N ARG L 265 " --> pdb=" O ILE L 261 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL L 275 " --> pdb=" O GLY L 271 " (cutoff:3.500A) Processing helix chain 'L' and resid 291 through 296 removed outlier: 4.119A pdb=" N TRP L 296 " --> pdb=" O TRP L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 302 removed outlier: 4.252A pdb=" N ASP L 300 " --> pdb=" O GLY L 297 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET L 302 " --> pdb=" O TRP L 299 " (cutoff:3.500A) Processing helix chain 'L' and resid 310 through 314 Processing helix chain 'M' and resid 337 through 344 removed outlier: 3.526A pdb=" N GLU M 341 " --> pdb=" O ASP M 337 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU M 342 " --> pdb=" O LEU M 338 " (cutoff:3.500A) Processing helix chain 'M' and resid 359 through 366 Processing helix chain 'M' and resid 380 through 400 removed outlier: 3.555A pdb=" N GLN M 400 " --> pdb=" O ASP M 396 " (cutoff:3.500A) Processing helix chain 'M' and resid 404 through 411 Processing helix chain 'M' and resid 412 through 415 removed outlier: 3.801A pdb=" N LEU M 415 " --> pdb=" O PHE M 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 412 through 415' Processing helix chain 'M' and resid 435 through 464 removed outlier: 3.735A pdb=" N LEU M 439 " --> pdb=" O GLY M 435 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA M 440 " --> pdb=" O GLY M 436 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA M 441 " --> pdb=" O ALA M 437 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR M 463 " --> pdb=" O ARG M 459 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY M 464 " --> pdb=" O ALA M 460 " (cutoff:3.500A) Processing helix chain 'M' and resid 467 through 485 removed outlier: 3.678A pdb=" N TRP M 471 " --> pdb=" O THR M 467 " (cutoff:3.500A) Processing helix chain 'M' and resid 493 through 497 removed outlier: 3.796A pdb=" N ALA M 496 " --> pdb=" O ASN M 493 " (cutoff:3.500A) Processing helix chain 'M' and resid 503 through 516 removed outlier: 3.665A pdb=" N TRP M 516 " --> pdb=" O VAL M 512 " (cutoff:3.500A) Processing helix chain 'M' and resid 518 through 521 Processing helix chain 'M' and resid 522 through 549 Processing helix chain 'M' and resid 550 through 553 Processing helix chain 'M' and resid 556 through 561 Processing helix chain 'M' and resid 565 through 580 removed outlier: 3.508A pdb=" N MET M 579 " --> pdb=" O TRP M 575 " (cutoff:3.500A) Processing helix chain 'M' and resid 586 through 613 removed outlier: 4.045A pdb=" N ILE M 590 " --> pdb=" O TYR M 586 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY M 611 " --> pdb=" O LEU M 607 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR M 612 " --> pdb=" O PHE M 608 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU M 613 " --> pdb=" O LEU M 609 " (cutoff:3.500A) Processing helix chain 'M' and resid 616 through 624 removed outlier: 3.648A pdb=" N THR M 623 " --> pdb=" O ALA M 619 " (cutoff:3.500A) Processing helix chain 'M' and resid 634 through 639 removed outlier: 4.056A pdb=" N GLN M 637 " --> pdb=" O ASP M 634 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL M 639 " --> pdb=" O ALA M 636 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 33 Processing helix chain 'O' and resid 21 through 51 removed outlier: 3.914A pdb=" N VAL O 25 " --> pdb=" O ALA O 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 34 removed outlier: 4.105A pdb=" N GLY P 34 " --> pdb=" O VAL P 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 20 through 51 removed outlier: 4.408A pdb=" N LEU Q 24 " --> pdb=" O ASN Q 20 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL Q 25 " --> pdb=" O ALA Q 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 7 through 33 Processing helix chain 'S' and resid 19 through 51 removed outlier: 3.674A pdb=" N TRP S 23 " --> pdb=" O ASN S 19 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU S 24 " --> pdb=" O ASN S 20 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 34 removed outlier: 4.008A pdb=" N GLY T 34 " --> pdb=" O VAL T 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 21 through 51 removed outlier: 4.075A pdb=" N VAL U 25 " --> pdb=" O ALA U 21 " (cutoff:3.500A) Processing helix chain 'V' and resid 7 through 33 Processing helix chain 'W' and resid 19 through 51 removed outlier: 3.601A pdb=" N TRP W 23 " --> pdb=" O ASN W 19 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU W 24 " --> pdb=" O ASN W 20 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL W 25 " --> pdb=" O ALA W 21 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 25 Processing helix chain 'Y' and resid 2 through 31 removed outlier: 4.007A pdb=" N ALA Y 6 " --> pdb=" O ASN Y 2 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE Y 17 " --> pdb=" O VAL Y 13 " (cutoff:3.500A) Proline residue: Y 19 - end of helix removed outlier: 3.963A pdb=" N ASN Y 31 " --> pdb=" O THR Y 27 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 47 removed outlier: 3.645A pdb=" N CYS Z 23 " --> pdb=" O GLY Z 19 " (cutoff:3.500A) Proline residue: Z 26 - end of helix Processing helix chain 'Z' and resid 53 through 58 removed outlier: 4.325A pdb=" N ASN Z 58 " --> pdb=" O PRO Z 54 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 7 through 9 removed outlier: 3.736A pdb=" N LEU L 16 " --> pdb=" O LEU L 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 33 through 34 removed outlier: 3.607A pdb=" N ILE L 34 " --> pdb=" O TYR Z 49 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR Z 49 " --> pdb=" O ILE L 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'L' and resid 62 through 64 removed outlier: 3.841A pdb=" N PHE L 62 " --> pdb=" O VAL L 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 350 through 351 1174 hydrogen bonds defined for protein. 3477 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.02 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.41: 10209 1.41 - 1.66: 14250 1.66 - 1.90: 126 1.90 - 2.14: 146 2.14 - 2.38: 61 Bond restraints: 24792 Sorted by residual: bond pdb=" C3C BPB M 704 " pdb=" CAC BPB M 704 " ideal model delta sigma weight residual 1.334 1.537 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C3C BPB L1003 " pdb=" CAC BPB L1003 " ideal model delta sigma weight residual 1.334 1.534 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" C3C BPB L1005 " pdb=" CAC BPB L1005 " ideal model delta sigma weight residual 1.334 1.531 -0.197 2.00e-02 2.50e+03 9.68e+01 bond pdb=" CAE KGD C 406 " pdb=" CAI KGD C 406 " ideal model delta sigma weight residual 1.502 1.387 0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" CAB KGD C 406 " pdb=" CAD KGD C 406 " ideal model delta sigma weight residual 1.528 1.435 0.093 2.00e-02 2.50e+03 2.18e+01 ... (remaining 24787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.11: 34079 4.11 - 8.21: 456 8.21 - 12.32: 22 12.32 - 16.43: 7 16.43 - 20.53: 3 Bond angle restraints: 34567 Sorted by residual: angle pdb=" N VAL L 314 " pdb=" CA VAL L 314 " pdb=" C VAL L 314 " ideal model delta sigma weight residual 108.11 116.41 -8.30 1.40e+00 5.10e-01 3.52e+01 angle pdb=" C2C BPB L1003 " pdb=" C3C BPB L1003 " pdb=" CAC BPB L1003 " ideal model delta sigma weight residual 127.33 110.95 16.38 3.00e+00 1.11e-01 2.98e+01 angle pdb=" C2C BPB L1005 " pdb=" C3C BPB L1005 " pdb=" CAC BPB L1005 " ideal model delta sigma weight residual 127.33 111.22 16.11 3.00e+00 1.11e-01 2.88e+01 angle pdb=" N GLU 1 7 " pdb=" CA GLU 1 7 " pdb=" C GLU 1 7 " ideal model delta sigma weight residual 111.28 117.12 -5.84 1.09e+00 8.42e-01 2.87e+01 angle pdb=" C2C BPB M 704 " pdb=" C3C BPB M 704 " pdb=" CAC BPB M 704 " ideal model delta sigma weight residual 127.33 111.31 16.02 3.00e+00 1.11e-01 2.85e+01 ... (remaining 34562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 12497 35.97 - 71.95: 393 71.95 - 107.92: 62 107.92 - 143.90: 14 143.90 - 179.87: 5 Dihedral angle restraints: 12971 sinusoidal: 6245 harmonic: 6726 Sorted by residual: dihedral pdb=" C1 BCL L1002 " pdb=" C2 BCL L1002 " pdb=" C3 BCL L1002 " pdb=" C5 BCL L1002 " ideal model delta sinusoidal sigma weight residual 180.00 0.13 179.87 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C2C HEM C 402 " pdb=" C3C HEM C 402 " pdb=" CAC HEM C 402 " pdb=" CBC HEM C 402 " ideal model delta sinusoidal sigma weight residual 180.00 91.94 88.06 2 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" C2B HEM C 403 " pdb=" C3B HEM C 403 " pdb=" CAB HEM C 403 " pdb=" CBB HEM C 403 " ideal model delta sinusoidal sigma weight residual 180.00 94.17 85.83 2 1.00e+01 1.00e-02 4.77e+01 ... (remaining 12968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3012 0.063 - 0.126: 384 0.126 - 0.189: 12 0.189 - 0.252: 1 0.252 - 0.315: 4 Chirality restraints: 3413 Sorted by residual: chirality pdb=" CA ASP 4 8 " pdb=" N ASP 4 8 " pdb=" C ASP 4 8 " pdb=" CB ASP 4 8 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA GLU 1 7 " pdb=" N GLU 1 7 " pdb=" C GLU 1 7 " pdb=" CB GLU 1 7 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA ASP L 243 " pdb=" N ASP L 243 " pdb=" C ASP L 243 " pdb=" CB ASP L 243 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 3410 not shown) Planarity restraints: 4217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2C BPB M 704 " -0.472 2.00e-02 2.50e+03 4.10e-01 2.10e+03 pdb=" C3C BPB M 704 " 0.491 2.00e-02 2.50e+03 pdb=" C4C BPB M 704 " -0.009 2.00e-02 2.50e+03 pdb=" CAC BPB M 704 " 0.428 2.00e-02 2.50e+03 pdb=" CBC BPB M 704 " -0.438 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2C BPB L1003 " 0.024 2.00e-02 2.50e+03 2.89e-01 1.04e+03 pdb=" C3C BPB L1003 " 0.323 2.00e-02 2.50e+03 pdb=" C4C BPB L1003 " -0.081 2.00e-02 2.50e+03 pdb=" CAC BPB L1003 " -0.501 2.00e-02 2.50e+03 pdb=" CBC BPB L1003 " 0.235 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2C BPB L1005 " 0.049 2.00e-02 2.50e+03 2.59e-01 8.37e+02 pdb=" C3C BPB L1005 " -0.446 2.00e-02 2.50e+03 pdb=" C4C BPB L1005 " 0.299 2.00e-02 2.50e+03 pdb=" CAC BPB L1005 " -0.091 2.00e-02 2.50e+03 pdb=" CBC BPB L1005 " 0.190 2.00e-02 2.50e+03 ... (remaining 4214 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 268 2.67 - 3.22: 20365 3.22 - 3.78: 35211 3.78 - 4.34: 49130 4.34 - 4.90: 82599 Nonbonded interactions: 187573 Sorted by model distance: nonbonded pdb=" SD MET C 229 " pdb="FE HEM C 404 " model vdw 2.107 3.360 nonbonded pdb=" O ILE L 189 " pdb=" OG1 THR L 190 " model vdw 2.208 3.040 nonbonded pdb=" SD MET C 106 " pdb="FE HEM C 402 " model vdw 2.226 3.360 nonbonded pdb=" OH TYR S 34 " pdb=" OBD BCL S 102 " model vdw 2.226 3.040 nonbonded pdb=" N GLU C 11 " pdb=" OE1 GLU C 11 " model vdw 2.276 3.120 ... (remaining 187568 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and resid 7 through 101) selection = (chain '2' and resid 7 through 101) selection = (chain '4' and resid 7 through 101) selection = (chain '6' and resid 7 through 101) selection = (chain '8' and resid 7 through 101) selection = (chain 'B' and resid 7 through 101) selection = (chain 'E' and resid 7 through 101) selection = (chain 'G' and resid 7 through 101) selection = (chain 'I' and resid 7 through 101) selection = (chain 'K' and resid 7 through 101) selection = (chain 'O' and resid 7 through 101) selection = (chain 'Q' and resid 7 through 101) selection = (chain 'S' and resid 7 through 101) selection = (chain 'U' and resid 7 through 101) selection = (chain 'W' and resid 7 through 101) } ncs_group { reference = (chain '1' and resid 4 through 41) selection = (chain '3' and resid 4 through 41) selection = (chain '5' and resid 4 through 41) selection = (chain '7' and resid 4 through 41) selection = (chain '9' and resid 4 through 41) selection = (chain 'A' and resid 4 through 41) selection = (chain 'D' and resid 4 through 41) selection = (chain 'F' and resid 4 through 41) selection = (chain 'H' and resid 4 through 41) selection = (chain 'J' and resid 4 through 41) selection = (chain 'N' and resid 4 through 41) selection = (chain 'P' and resid 4 through 41) selection = (chain 'R' and resid 4 through 41) selection = (chain 'T' and resid 4 through 41) selection = (chain 'V' and resid 4 through 41) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.430 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 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 : 0.010 0.403 24852 Z= 0.716 Angle : 1.019 20.533 34567 Z= 0.402 Chirality : 0.041 0.315 3413 Planarity : 0.011 0.410 4217 Dihedral : 18.338 179.869 8599 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.46 % Favored : 96.50 % Rotamer: Outliers : 0.30 % Allowed : 0.30 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.18), residues: 2257 helix: 3.22 (0.13), residues: 1403 sheet: 1.12 (1.93), residues: 8 loop : -1.99 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 2 55 TYR 0.036 0.001 TYR C 21 PHE 0.028 0.001 PHE M 391 TRP 0.019 0.001 TRP M 594 HIS 0.010 0.001 HIS 1 27 Details of bonding type rmsd covalent geometry : bond 0.00689 (24792) covalent geometry : angle 1.01922 (34567) hydrogen bonds : bond 0.13531 ( 1174) hydrogen bonds : angle 4.23777 ( 3477) Misc. bond : bond 0.13345 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 369 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: B 22 GLN cc_start: 0.7256 (mt0) cc_final: 0.6942 (mt0) REVERT: C 73 GLU cc_start: 0.6342 (pp20) cc_final: 0.5406 (pm20) REVERT: H 16 THR cc_start: 0.8886 (m) cc_final: 0.8678 (m) REVERT: L 308 VAL cc_start: 0.7548 (m) cc_final: 0.7343 (t) REVERT: T 32 SER cc_start: 0.9023 (p) cc_final: 0.8649 (m) REVERT: U 31 LYS cc_start: 0.8129 (mtpt) cc_final: 0.7833 (mtmt) REVERT: W 24 LEU cc_start: 0.8260 (mp) cc_final: 0.8012 (mt) REVERT: X 1 MET cc_start: 0.5758 (mtp) cc_final: 0.4852 (mmp) REVERT: Z 46 THR cc_start: 0.7838 (m) cc_final: 0.7615 (m) outliers start: 6 outliers final: 3 residues processed: 372 average time/residue: 0.1677 time to fit residues: 99.5824 Evaluate side-chains 278 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 275 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 7 ASN Chi-restraints excluded: chain 6 residue 8 ASP Chi-restraints excluded: chain C residue 145 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 ASN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN L 198 ASN L 205 ASN L 264 HIS L 293 ASN M 493 ASN O 20 ASN Q 20 ASN U 7 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.108423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.091630 restraints weight = 37845.634| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.24 r_work: 0.2879 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.270 24852 Z= 0.184 Angle : 0.793 12.818 34567 Z= 0.319 Chirality : 0.042 0.215 3413 Planarity : 0.005 0.069 4217 Dihedral : 18.621 179.847 4594 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.94 % Favored : 96.01 % Rotamer: Outliers : 2.18 % Allowed : 6.65 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.18), residues: 2257 helix: 3.23 (0.13), residues: 1411 sheet: 0.53 (1.63), residues: 8 loop : -1.91 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 17 TYR 0.017 0.001 TYR C 21 PHE 0.016 0.001 PHE L 185 TRP 0.015 0.001 TRP O 50 HIS 0.005 0.001 HIS M 487 Details of bonding type rmsd covalent geometry : bond 0.00455 (24792) covalent geometry : angle 0.79296 (34567) hydrogen bonds : bond 0.06813 ( 1174) hydrogen bonds : angle 3.54395 ( 3477) Misc. bond : bond 0.04428 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 269 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: K 27 ASP cc_start: 0.7963 (t0) cc_final: 0.7737 (t0) REVERT: L 308 VAL cc_start: 0.7674 (m) cc_final: 0.7453 (t) REVERT: M 553 LYS cc_start: 0.7671 (mmmt) cc_final: 0.7383 (mttm) REVERT: U 31 LYS cc_start: 0.8178 (mtpt) cc_final: 0.7944 (mtmt) REVERT: W 24 LEU cc_start: 0.8286 (mp) cc_final: 0.8077 (mt) REVERT: X 6 MET cc_start: 0.6813 (mtm) cc_final: 0.6426 (mmm) REVERT: X 21 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7499 (mp) outliers start: 43 outliers final: 33 residues processed: 297 average time/residue: 0.1590 time to fit residues: 77.3562 Evaluate side-chains 289 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 255 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 45 VAL Chi-restraints excluded: chain 2 residue 10 VAL Chi-restraints excluded: chain 4 residue 32 THR Chi-restraints excluded: chain 5 residue 15 SER Chi-restraints excluded: chain 5 residue 24 LEU Chi-restraints excluded: chain 6 residue 41 VAL Chi-restraints excluded: chain 6 residue 45 VAL Chi-restraints excluded: chain 9 residue 21 VAL Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain D residue 6 PHE Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 103 MET Chi-restraints excluded: chain M residue 539 LEU Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain U residue 7 ASN Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Z residue 22 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 89 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 170 optimal weight: 9.9990 chunk 160 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 167 optimal weight: 10.0000 chunk 173 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 7 ASN B 20 ASN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.108377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.092320 restraints weight = 37941.977| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.39 r_work: 0.2854 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.167 24852 Z= 0.153 Angle : 0.731 12.517 34567 Z= 0.293 Chirality : 0.040 0.190 3413 Planarity : 0.005 0.059 4217 Dihedral : 17.669 179.895 4590 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.99 % Favored : 95.97 % Rotamer: Outliers : 2.49 % Allowed : 8.52 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.37 (0.18), residues: 2257 helix: 3.36 (0.13), residues: 1413 sheet: -0.12 (1.26), residues: 8 loop : -1.82 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 2 55 TYR 0.010 0.001 TYR M 521 PHE 0.015 0.001 PHE L 185 TRP 0.014 0.001 TRP M 594 HIS 0.004 0.001 HIS M 487 Details of bonding type rmsd covalent geometry : bond 0.00375 (24792) covalent geometry : angle 0.73099 (34567) hydrogen bonds : bond 0.06243 ( 1174) hydrogen bonds : angle 3.36551 ( 3477) Misc. bond : bond 0.02818 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 269 time to evaluate : 0.825 Fit side-chains REVERT: C 21 TYR cc_start: 0.6878 (m-80) cc_final: 0.6492 (m-80) REVERT: C 89 GLN cc_start: 0.7849 (mt0) cc_final: 0.7372 (mp10) REVERT: C 106 MET cc_start: 0.8854 (mmt) cc_final: 0.7860 (mmt) REVERT: M 553 LYS cc_start: 0.7710 (mmmt) cc_final: 0.7308 (mttm) REVERT: S 9 LEU cc_start: 0.7552 (mt) cc_final: 0.7330 (mt) REVERT: U 31 LYS cc_start: 0.8187 (mtpt) cc_final: 0.7969 (mtmt) REVERT: X 21 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7569 (mp) REVERT: Z 22 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.7045 (mp) outliers start: 49 outliers final: 39 residues processed: 299 average time/residue: 0.1612 time to fit residues: 78.3760 Evaluate side-chains 301 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 260 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 45 VAL Chi-restraints excluded: chain 2 residue 10 VAL Chi-restraints excluded: chain 4 residue 7 ASN Chi-restraints excluded: chain 4 residue 32 THR Chi-restraints excluded: chain 5 residue 15 SER Chi-restraints excluded: chain 5 residue 24 LEU Chi-restraints excluded: chain 6 residue 41 VAL Chi-restraints excluded: chain 6 residue 45 VAL Chi-restraints excluded: chain 7 residue 29 VAL Chi-restraints excluded: chain 8 residue 27 ASP Chi-restraints excluded: chain 9 residue 21 VAL Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain D residue 6 PHE Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain M residue 539 LEU Chi-restraints excluded: chain M residue 561 MET Chi-restraints excluded: chain M residue 609 LEU Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Z residue 22 LEU Chi-restraints excluded: chain Z residue 46 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 166 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 148 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 27 HIS 4 13 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 7 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.106037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.089721 restraints weight = 37648.213| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.34 r_work: 0.2808 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.314 24852 Z= 0.275 Angle : 0.798 13.967 34567 Z= 0.318 Chirality : 0.042 0.215 3413 Planarity : 0.005 0.056 4217 Dihedral : 17.506 179.796 4590 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.25 % Favored : 95.70 % Rotamer: Outliers : 2.89 % Allowed : 10.35 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.18), residues: 2257 helix: 3.17 (0.13), residues: 1415 sheet: -0.60 (1.13), residues: 8 loop : -1.81 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG V 40 TYR 0.014 0.002 TYR M 424 PHE 0.017 0.001 PHE L 185 TRP 0.014 0.001 TRP M 594 HIS 0.007 0.001 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00471 (24792) covalent geometry : angle 0.79778 (34567) hydrogen bonds : bond 0.07120 ( 1174) hydrogen bonds : angle 3.47241 ( 3477) Misc. bond : bond 0.04910 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 265 time to evaluate : 0.782 Fit side-chains REVERT: C 73 GLU cc_start: 0.6832 (pp20) cc_final: 0.5899 (pt0) REVERT: C 89 GLN cc_start: 0.7944 (mt0) cc_final: 0.7431 (mp10) REVERT: C 106 MET cc_start: 0.8843 (mmt) cc_final: 0.7842 (mmt) REVERT: M 519 PHE cc_start: 0.9148 (OUTLIER) cc_final: 0.8928 (t80) REVERT: M 553 LYS cc_start: 0.7701 (mmmt) cc_final: 0.7409 (mttm) REVERT: U 15 LYS cc_start: 0.8230 (tppt) cc_final: 0.8011 (mmmt) REVERT: U 31 LYS cc_start: 0.8184 (mtpt) cc_final: 0.7979 (mtmt) REVERT: X 21 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7555 (mp) REVERT: Z 22 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7296 (mp) outliers start: 57 outliers final: 41 residues processed: 297 average time/residue: 0.1344 time to fit residues: 65.0317 Evaluate side-chains 300 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 256 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 45 VAL Chi-restraints excluded: chain 2 residue 10 VAL Chi-restraints excluded: chain 4 residue 32 THR Chi-restraints excluded: chain 5 residue 15 SER Chi-restraints excluded: chain 5 residue 24 LEU Chi-restraints excluded: chain 6 residue 41 VAL Chi-restraints excluded: chain 6 residue 45 VAL Chi-restraints excluded: chain 9 residue 21 VAL Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain M residue 423 GLU Chi-restraints excluded: chain M residue 519 PHE Chi-restraints excluded: chain M residue 539 LEU Chi-restraints excluded: chain M residue 561 MET Chi-restraints excluded: chain M residue 609 LEU Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain U residue 7 ASN Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Z residue 22 LEU Chi-restraints excluded: chain Z residue 46 THR Chi-restraints excluded: chain Z residue 50 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 101 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 150 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 181 optimal weight: 0.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 ASN C 154 GLN S 20 ASN U 7 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.107900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.091637 restraints weight = 37403.364| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.35 r_work: 0.2844 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.161 24852 Z= 0.142 Angle : 0.711 11.994 34567 Z= 0.283 Chirality : 0.039 0.177 3413 Planarity : 0.005 0.051 4217 Dihedral : 17.105 179.916 4590 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.49 % Allowed : 11.01 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.47 (0.18), residues: 2257 helix: 3.41 (0.13), residues: 1414 sheet: -0.68 (1.12), residues: 8 loop : -1.71 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG V 40 TYR 0.009 0.001 TYR M 521 PHE 0.014 0.001 PHE L 185 TRP 0.015 0.001 TRP M 594 HIS 0.004 0.001 HIS 3 27 Details of bonding type rmsd covalent geometry : bond 0.00339 (24792) covalent geometry : angle 0.71126 (34567) hydrogen bonds : bond 0.06137 ( 1174) hydrogen bonds : angle 3.33341 ( 3477) Misc. bond : bond 0.02387 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 263 time to evaluate : 0.814 Fit side-chains REVERT: C 89 GLN cc_start: 0.7931 (mt0) cc_final: 0.7434 (mp10) REVERT: C 106 MET cc_start: 0.8829 (mmt) cc_final: 0.7887 (mmt) REVERT: E 13 GLN cc_start: 0.7013 (tp40) cc_final: 0.6695 (tp40) REVERT: M 553 LYS cc_start: 0.7665 (mmmt) cc_final: 0.7365 (mttm) REVERT: U 31 LYS cc_start: 0.8185 (mtpt) cc_final: 0.7971 (mtmt) REVERT: X 21 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7507 (mp) outliers start: 49 outliers final: 43 residues processed: 290 average time/residue: 0.1510 time to fit residues: 71.4011 Evaluate side-chains 301 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 257 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 45 VAL Chi-restraints excluded: chain 4 residue 32 THR Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 5 residue 15 SER Chi-restraints excluded: chain 5 residue 24 LEU Chi-restraints excluded: chain 6 residue 41 VAL Chi-restraints excluded: chain 7 residue 29 VAL Chi-restraints excluded: chain 8 residue 27 ASP Chi-restraints excluded: chain 9 residue 21 VAL Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain M residue 423 GLU Chi-restraints excluded: chain M residue 539 LEU Chi-restraints excluded: chain M residue 561 MET Chi-restraints excluded: chain M residue 609 LEU Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain Q residue 10 VAL Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain S residue 20 ASN Chi-restraints excluded: chain U residue 7 ASN Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Z residue 46 THR Chi-restraints excluded: chain Z residue 50 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 8 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 199 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 chunk 163 optimal weight: 10.0000 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.106249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.089923 restraints weight = 37795.045| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.35 r_work: 0.2816 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.177 24852 Z= 0.186 Angle : 0.769 13.150 34567 Z= 0.305 Chirality : 0.042 0.195 3413 Planarity : 0.005 0.054 4217 Dihedral : 17.144 179.817 4590 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.59 % Allowed : 11.67 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.18), residues: 2257 helix: 3.24 (0.13), residues: 1415 sheet: -0.58 (1.22), residues: 8 loop : -1.76 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 9 TYR 0.015 0.002 TYR M 424 PHE 0.017 0.001 PHE L 185 TRP 0.014 0.001 TRP M 594 HIS 0.006 0.001 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00463 (24792) covalent geometry : angle 0.76887 (34567) hydrogen bonds : bond 0.06829 ( 1174) hydrogen bonds : angle 3.41665 ( 3477) Misc. bond : bond 0.02471 ( 60) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 253 time to evaluate : 0.579 Fit side-chains REVERT: C 106 MET cc_start: 0.8838 (mmt) cc_final: 0.7864 (mmt) REVERT: E 13 GLN cc_start: 0.7138 (tp40) cc_final: 0.6838 (tp40) REVERT: M 519 PHE cc_start: 0.9148 (OUTLIER) cc_final: 0.8941 (t80) REVERT: M 553 LYS cc_start: 0.7702 (mmmt) cc_final: 0.7409 (mttm) REVERT: U 31 LYS cc_start: 0.8203 (mtpt) cc_final: 0.7996 (mtmt) REVERT: X 21 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7487 (mp) outliers start: 51 outliers final: 44 residues processed: 283 average time/residue: 0.1277 time to fit residues: 59.0007 Evaluate side-chains 295 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 249 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 45 VAL Chi-restraints excluded: chain 4 residue 32 THR Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 5 residue 15 SER Chi-restraints excluded: chain 5 residue 24 LEU Chi-restraints excluded: chain 6 residue 41 VAL Chi-restraints excluded: chain 6 residue 45 VAL Chi-restraints excluded: chain 8 residue 27 ASP Chi-restraints excluded: chain 9 residue 21 VAL Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain M residue 423 GLU Chi-restraints excluded: chain M residue 519 PHE Chi-restraints excluded: chain M residue 539 LEU Chi-restraints excluded: chain M residue 561 MET Chi-restraints excluded: chain M residue 609 LEU Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain Q residue 10 VAL Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Z residue 46 THR Chi-restraints excluded: chain Z residue 50 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 65 optimal weight: 0.0770 chunk 11 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 183 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 53 optimal weight: 50.0000 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 13 GLN C 56 ASN S 20 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.108954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.092708 restraints weight = 37311.512| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.39 r_work: 0.2860 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.139 24852 Z= 0.130 Angle : 0.679 11.354 34567 Z= 0.272 Chirality : 0.039 0.161 3413 Planarity : 0.005 0.052 4217 Dihedral : 16.636 179.923 4590 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.03 % Allowed : 12.99 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.61 (0.18), residues: 2257 helix: 3.53 (0.13), residues: 1414 sheet: -0.86 (1.15), residues: 8 loop : -1.68 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 7 40 TYR 0.009 0.001 TYR C 230 PHE 0.013 0.001 PHE L 185 TRP 0.015 0.001 TRP M 594 HIS 0.004 0.001 HIS 3 27 Details of bonding type rmsd covalent geometry : bond 0.00308 (24792) covalent geometry : angle 0.67932 (34567) hydrogen bonds : bond 0.05591 ( 1174) hydrogen bonds : angle 3.24005 ( 3477) Misc. bond : bond 0.02114 ( 60) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 254 time to evaluate : 0.498 Fit side-chains REVERT: 1 20 LEU cc_start: 0.8364 (tp) cc_final: 0.7737 (mt) REVERT: B 22 GLN cc_start: 0.7578 (mt0) cc_final: 0.7321 (mt0) REVERT: C 106 MET cc_start: 0.8799 (mmt) cc_final: 0.7862 (mmt) REVERT: M 519 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.8894 (t80) REVERT: M 553 LYS cc_start: 0.7675 (mmmt) cc_final: 0.7390 (mttm) REVERT: U 31 LYS cc_start: 0.8202 (mtpt) cc_final: 0.7985 (mtmt) outliers start: 40 outliers final: 34 residues processed: 279 average time/residue: 0.1287 time to fit residues: 58.9020 Evaluate side-chains 285 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 250 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 45 VAL Chi-restraints excluded: chain 4 residue 32 THR Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 5 residue 15 SER Chi-restraints excluded: chain 5 residue 24 LEU Chi-restraints excluded: chain 6 residue 41 VAL Chi-restraints excluded: chain 6 residue 45 VAL Chi-restraints excluded: chain 7 residue 29 VAL Chi-restraints excluded: chain 8 residue 27 ASP Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 281 CYS Chi-restraints excluded: chain M residue 423 GLU Chi-restraints excluded: chain M residue 519 PHE Chi-restraints excluded: chain M residue 539 LEU Chi-restraints excluded: chain M residue 561 MET Chi-restraints excluded: chain M residue 609 LEU Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Z residue 46 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 148 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 204 optimal weight: 8.9990 chunk 59 optimal weight: 0.2980 chunk 150 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 163 optimal weight: 9.9990 chunk 84 optimal weight: 0.6980 chunk 28 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 13 GLN U 19 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.107922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.091581 restraints weight = 37518.812| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.40 r_work: 0.2840 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.171 24852 Z= 0.143 Angle : 0.700 12.188 34567 Z= 0.279 Chirality : 0.039 0.172 3413 Planarity : 0.005 0.050 4217 Dihedral : 16.482 179.885 4587 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.98 % Allowed : 13.34 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.53 (0.18), residues: 2257 helix: 3.44 (0.13), residues: 1416 sheet: -0.54 (1.29), residues: 8 loop : -1.66 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 53 TYR 0.013 0.001 TYR M 424 PHE 0.015 0.001 PHE L 185 TRP 0.013 0.001 TRP M 594 HIS 0.005 0.001 HIS L 192 Details of bonding type rmsd covalent geometry : bond 0.00345 (24792) covalent geometry : angle 0.69976 (34567) hydrogen bonds : bond 0.05943 ( 1174) hydrogen bonds : angle 3.27988 ( 3477) Misc. bond : bond 0.02286 ( 60) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 258 time to evaluate : 0.506 Fit side-chains REVERT: C 89 GLN cc_start: 0.8060 (mt0) cc_final: 0.7647 (mp10) REVERT: C 106 MET cc_start: 0.8794 (mmt) cc_final: 0.7831 (mmt) REVERT: G 7 ASN cc_start: 0.6274 (p0) cc_final: 0.5869 (p0) REVERT: M 519 PHE cc_start: 0.9126 (OUTLIER) cc_final: 0.8904 (t80) REVERT: M 553 LYS cc_start: 0.7700 (mmmt) cc_final: 0.7421 (mttm) REVERT: U 31 LYS cc_start: 0.8205 (mtpt) cc_final: 0.7997 (mtmt) REVERT: X 21 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7472 (mp) REVERT: Y 17 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.6594 (t80) outliers start: 39 outliers final: 34 residues processed: 282 average time/residue: 0.1273 time to fit residues: 59.1309 Evaluate side-chains 289 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 252 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 45 VAL Chi-restraints excluded: chain 4 residue 32 THR Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 5 residue 15 SER Chi-restraints excluded: chain 5 residue 24 LEU Chi-restraints excluded: chain 6 residue 41 VAL Chi-restraints excluded: chain 6 residue 45 VAL Chi-restraints excluded: chain 7 residue 29 VAL Chi-restraints excluded: chain 8 residue 27 ASP Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain M residue 423 GLU Chi-restraints excluded: chain M residue 519 PHE Chi-restraints excluded: chain M residue 539 LEU Chi-restraints excluded: chain M residue 561 MET Chi-restraints excluded: chain M residue 609 LEU Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain Q residue 10 VAL Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain Y residue 17 PHE Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Z residue 46 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 96 optimal weight: 8.9990 chunk 202 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 187 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 167 optimal weight: 9.9990 chunk 180 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 13 GLN B 20 ASN ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 572 GLN M 582 ASN U 19 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.104109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.087734 restraints weight = 37889.536| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.36 r_work: 0.2781 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.206 24852 Z= 0.228 Angle : 0.842 14.795 34567 Z= 0.338 Chirality : 0.044 0.237 3413 Planarity : 0.005 0.055 4217 Dihedral : 17.165 179.787 4587 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.33 % Allowed : 13.34 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.18), residues: 2257 helix: 3.01 (0.13), residues: 1418 sheet: -0.30 (1.45), residues: 8 loop : -1.77 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 55 TYR 0.024 0.002 TYR M 424 PHE 0.017 0.002 PHE L 185 TRP 0.028 0.002 TRP V 38 HIS 0.007 0.001 HIS L 183 Details of bonding type rmsd covalent geometry : bond 0.00572 (24792) covalent geometry : angle 0.84182 (34567) hydrogen bonds : bond 0.07898 ( 1174) hydrogen bonds : angle 3.57187 ( 3477) Misc. bond : bond 0.02765 ( 60) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 255 time to evaluate : 0.754 Fit side-chains REVERT: C 73 GLU cc_start: 0.6786 (pp20) cc_final: 0.6294 (pt0) REVERT: C 89 GLN cc_start: 0.8031 (mt0) cc_final: 0.7615 (mp10) REVERT: C 106 MET cc_start: 0.8833 (mmt) cc_final: 0.7806 (mmt) REVERT: C 247 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.7280 (ptm160) REVERT: G 7 ASN cc_start: 0.6421 (p0) cc_final: 0.6051 (p0) REVERT: M 553 LYS cc_start: 0.7780 (mmmt) cc_final: 0.7453 (mttm) REVERT: U 31 LYS cc_start: 0.8199 (mtpt) cc_final: 0.7993 (mtmt) REVERT: X 21 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7436 (mp) outliers start: 46 outliers final: 35 residues processed: 285 average time/residue: 0.1453 time to fit residues: 66.9048 Evaluate side-chains 289 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 252 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 45 VAL Chi-restraints excluded: chain 4 residue 32 THR Chi-restraints excluded: chain 5 residue 15 SER Chi-restraints excluded: chain 6 residue 41 VAL Chi-restraints excluded: chain 6 residue 45 VAL Chi-restraints excluded: chain 8 residue 27 ASP Chi-restraints excluded: chain 9 residue 21 VAL Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain M residue 423 GLU Chi-restraints excluded: chain M residue 539 LEU Chi-restraints excluded: chain M residue 561 MET Chi-restraints excluded: chain M residue 609 LEU Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain Q residue 10 VAL Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Z residue 46 THR Chi-restraints excluded: chain Z residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 76 optimal weight: 0.0870 chunk 43 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 196 optimal weight: 4.9990 overall best weight: 1.7164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 13 GLN B 13 GLN B 22 GLN U 19 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.108512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.092322 restraints weight = 37634.547| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.40 r_work: 0.2854 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.162 24852 Z= 0.128 Angle : 0.680 12.046 34567 Z= 0.274 Chirality : 0.039 0.151 3413 Planarity : 0.005 0.047 4217 Dihedral : 16.450 179.962 4587 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.32 % Allowed : 14.66 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.56 (0.18), residues: 2257 helix: 3.49 (0.13), residues: 1415 sheet: -0.60 (1.31), residues: 8 loop : -1.70 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 280 TYR 0.008 0.001 TYR C 230 PHE 0.012 0.001 PHE Y 17 TRP 0.015 0.001 TRP M 594 HIS 0.005 0.001 HIS 3 27 Details of bonding type rmsd covalent geometry : bond 0.00296 (24792) covalent geometry : angle 0.67962 (34567) hydrogen bonds : bond 0.05604 ( 1174) hydrogen bonds : angle 3.26105 ( 3477) Misc. bond : bond 0.02316 ( 60) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 257 time to evaluate : 0.989 Fit side-chains REVERT: 1 20 LEU cc_start: 0.8376 (tp) cc_final: 0.7741 (mt) REVERT: C 73 GLU cc_start: 0.6753 (pp20) cc_final: 0.6320 (pt0) REVERT: C 89 GLN cc_start: 0.8056 (mt0) cc_final: 0.7656 (mp10) REVERT: C 106 MET cc_start: 0.8772 (mmt) cc_final: 0.7875 (mmt) REVERT: C 247 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.7244 (ptm160) REVERT: G 7 ASN cc_start: 0.6364 (p0) cc_final: 0.6050 (p0) REVERT: M 553 LYS cc_start: 0.7656 (mmmt) cc_final: 0.7385 (mttm) REVERT: U 31 LYS cc_start: 0.8198 (mtpt) cc_final: 0.7989 (mtmt) outliers start: 26 outliers final: 25 residues processed: 272 average time/residue: 0.1355 time to fit residues: 60.3162 Evaluate side-chains 281 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 255 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 45 VAL Chi-restraints excluded: chain 4 residue 32 THR Chi-restraints excluded: chain 5 residue 15 SER Chi-restraints excluded: chain 6 residue 41 VAL Chi-restraints excluded: chain 6 residue 45 VAL Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain M residue 539 LEU Chi-restraints excluded: chain M residue 609 LEU Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Z residue 46 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 141 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 190 optimal weight: 7.9990 chunk 184 optimal weight: 8.9990 chunk 174 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 13 GLN B 20 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.106874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.090716 restraints weight = 37639.638| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.48 r_work: 0.2818 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.177 24852 Z= 0.161 Angle : 0.728 12.720 34567 Z= 0.293 Chirality : 0.041 0.186 3413 Planarity : 0.005 0.050 4217 Dihedral : 16.495 179.858 4587 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.73 % Allowed : 14.26 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.42 (0.18), residues: 2257 helix: 3.35 (0.13), residues: 1417 sheet: -0.39 (1.41), residues: 8 loop : -1.72 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 280 TYR 0.015 0.001 TYR M 424 PHE 0.017 0.001 PHE L 185 TRP 0.019 0.001 TRP V 38 HIS 0.005 0.001 HIS L 192 Details of bonding type rmsd covalent geometry : bond 0.00394 (24792) covalent geometry : angle 0.72757 (34567) hydrogen bonds : bond 0.06346 ( 1174) hydrogen bonds : angle 3.34191 ( 3477) Misc. bond : bond 0.02397 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5476.05 seconds wall clock time: 94 minutes 13.26 seconds (5653.26 seconds total)