Starting phenix.real_space_refine on Mon Aug 25 04:49:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hju_34838/08_2025/8hju_34838.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hju_34838/08_2025/8hju_34838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hju_34838/08_2025/8hju_34838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hju_34838/08_2025/8hju_34838.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hju_34838/08_2025/8hju_34838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hju_34838/08_2025/8hju_34838.map" } resolution = 2.8 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= 0.008 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 7 5.49 5 Mg 48 5.21 5 S 75 5.16 5 C 17010 2.51 5 N 3312 2.21 5 O 3460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.01s 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: 23917 Number of models: 1 Model: "" Number of chains: 71 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: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 271 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} 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: "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: 2389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2389 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 16, 'TRANS': 285} 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: "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: "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: 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: "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: 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: "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: 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: "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: 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: "B" 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: "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: 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: "F" 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: "G" 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: "H" 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: "I" 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: "J" 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: "K" 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: "L" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 404 Unusual residues: {'BCL': 2, 'BPH': 2, 'MQE': 1, 'PGV': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 258 Unusual residues: {' FE': 1, 'BCL': 1, 'BPH': 1, 'MQE': 2, 'PGV': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 55 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, 'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 48 Chain: "N" 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: "O" 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: "P" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 185 Unusual residues: {'BCL': 1, 'KGD': 1, 'PGV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'PGV:plan-3': 2} Unresolved non-hydrogen planarities: 5 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "S" 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: "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: "W" 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: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 258 Unusual residues: {'HEM': 4, 'KGD': 1, 'PGV': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "X" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'DGA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PGV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 5.70, per 1000 atoms: 0.24 Number of scatterers: 23917 At special positions: 0 Unit cell: (138.24, 122.04, 143.64, 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 7 15.00 Mg 48 11.99 O 3460 8.00 N 3312 7.00 C 17010 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=61, symmetry=0 Number of additional bonds: simple=61, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 1.4 microseconds 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4370 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 3 sheets defined 68.9% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain '0' and resid 19 through 51 removed outlier: 3.834A pdb=" N LEU 0 24 " --> pdb=" O ASN 0 20 " (cutoff:3.500A) Processing helix chain '1' and resid 8 through 33 Processing helix chain '2' and resid 19 through 51 removed outlier: 3.834A pdb=" N LEU 2 24 " --> pdb=" O ASN 2 20 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 34 removed outlier: 3.975A pdb=" N GLY 3 34 " --> pdb=" O VAL 3 30 " (cutoff:3.500A) Processing helix chain '4' and resid 19 through 51 removed outlier: 3.834A pdb=" N LEU 4 24 " --> pdb=" O ASN 4 20 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY 5 34 " --> pdb=" O VAL 5 30 " (cutoff:3.500A) Processing helix chain '6' and resid 19 through 51 removed outlier: 3.834A pdb=" N LEU 6 24 " --> pdb=" O ASN 6 20 " (cutoff:3.500A) Processing helix chain '7' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY 7 34 " --> pdb=" O VAL 7 30 " (cutoff:3.500A) Processing helix chain '8' and resid 19 through 51 removed outlier: 3.833A pdb=" N LEU 8 24 " --> pdb=" O ASN 8 20 " (cutoff:3.500A) Processing helix chain '9' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY 9 34 " --> pdb=" O VAL 9 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 15 Processing helix chain 'B' and resid 19 through 51 removed outlier: 3.834A pdb=" N LEU B 24 " --> pdb=" O ASN B 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY D 34 " --> pdb=" O VAL D 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 15 Processing helix chain 'E' and resid 19 through 51 removed outlier: 3.833A pdb=" N LEU E 24 " --> pdb=" O ASN E 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY F 34 " --> pdb=" O VAL F 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 51 removed outlier: 3.833A pdb=" N LEU G 24 " --> pdb=" O ASN G 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY H 34 " --> pdb=" O VAL H 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 15 Processing helix chain 'I' and resid 19 through 51 removed outlier: 3.834A pdb=" N LEU I 24 " --> pdb=" O ASN I 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY J 34 " --> pdb=" O VAL J 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 51 removed outlier: 3.833A pdb=" N LEU K 24 " --> pdb=" O ASN K 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 43 Processing helix chain 'L' and resid 49 through 55 Processing helix chain 'L' and resid 70 through 93 removed outlier: 4.108A 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 Processing helix chain 'L' and resid 154 through 172 Processing helix chain 'L' and resid 172 through 179 Processing helix chain 'L' and resid 191 through 203 Processing helix chain 'L' and resid 205 through 208 Processing helix chain 'L' and resid 209 through 236 Processing helix chain 'L' and resid 244 through 253 Processing helix chain 'L' and resid 259 through 288 removed outlier: 3.780A pdb=" N HIS L 264 " --> pdb=" O GLU L 260 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL L 275 " --> pdb=" O GLY L 271 " (cutoff:3.500A) Processing helix chain 'L' and resid 291 through 296 removed outlier: 4.031A pdb=" N TRP L 296 " --> pdb=" O TRP L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 302 removed outlier: 4.036A pdb=" N ASP L 300 " --> pdb=" O GLY L 297 " (cutoff:3.500A) Processing helix chain 'L' and resid 310 through 314 removed outlier: 3.869A pdb=" N VAL L 314 " --> pdb=" O GLY L 311 " (cutoff:3.500A) Processing helix chain 'M' and resid 337 through 344 Processing helix chain 'M' and resid 359 through 366 Processing helix chain 'M' and resid 378 through 401 Processing helix chain 'M' and resid 404 through 412 removed outlier: 3.512A pdb=" N LEU M 409 " --> pdb=" O PRO M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 435 through 463 removed outlier: 3.576A pdb=" N ALA M 440 " --> pdb=" O GLY M 436 " (cutoff:3.500A) Processing helix chain 'M' and resid 467 through 485 Processing helix chain 'M' and resid 493 through 497 removed outlier: 3.558A pdb=" N ALA M 496 " --> pdb=" O ASN M 493 " (cutoff:3.500A) Processing helix chain 'M' and resid 503 through 516 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 Processing helix chain 'M' and resid 586 through 613 removed outlier: 3.602A pdb=" N ILE M 590 " --> pdb=" O TYR M 586 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY M 611 " --> pdb=" O LEU M 607 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR M 612 " --> pdb=" O PHE M 608 " (cutoff:3.500A) Processing helix chain 'M' and resid 616 through 624 Processing helix chain 'N' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY N 34 " --> pdb=" O VAL N 30 " (cutoff:3.500A) Processing helix chain 'O' and resid 19 through 51 removed outlier: 3.834A pdb=" N LEU O 24 " --> pdb=" O ASN O 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY P 34 " --> pdb=" O VAL P 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 19 through 51 removed outlier: 3.834A pdb=" N LEU Q 24 " --> pdb=" O ASN Q 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY R 34 " --> pdb=" O VAL R 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 19 through 51 removed outlier: 3.834A pdb=" N LEU S 24 " --> pdb=" O ASN S 20 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY T 34 " --> pdb=" O VAL T 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 11 through 15 Processing helix chain 'U' and resid 19 through 51 removed outlier: 3.834A pdb=" N LEU U 24 " --> pdb=" O ASN U 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 7 through 33 Processing helix chain 'V' and resid 36 through 40 Processing helix chain 'W' and resid 19 through 51 removed outlier: 3.834A pdb=" N LEU W 24 " --> pdb=" O ASN W 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 14 Processing helix chain 'C' and resid 15 through 47 removed outlier: 3.650A pdb=" N ILE C 22 " --> pdb=" O GLY C 18 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 85 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: 3.509A pdb=" N LYS C 139 " --> pdb=" O ASN C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 175 removed outlier: 3.920A pdb=" N CYS C 174 " --> pdb=" O THR C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 236 Processing helix chain 'C' and resid 239 through 243 removed outlier: 3.506A pdb=" N PHE C 242 " --> pdb=" O GLY C 239 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N CYS C 243 " --> pdb=" O CYS C 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 239 through 243' Processing helix chain 'C' and resid 255 through 274 removed outlier: 3.593A pdb=" N HIS C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 289 removed outlier: 4.323A pdb=" N GLY C 288 " --> pdb=" O ILE C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 298 removed outlier: 4.430A pdb=" N CYS C 296 " --> pdb=" O SER C 292 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 25 Processing helix chain 'Y' and resid 2 through 31 Proline residue: Y 19 - end of helix Processing helix chain 'Z' and resid 16 through 47 Proline residue: Z 26 - end of helix Processing helix chain 'Z' and resid 53 through 58 Processing sheet with id=AA1, first strand: chain 'L' and resid 32 through 34 removed outlier: 3.992A pdb=" N TYR Z 49 " --> pdb=" O ILE L 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 62 through 64 removed outlier: 3.868A pdb=" N PHE L 62 " --> pdb=" O VAL L 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 349 through 351 removed outlier: 3.766A pdb=" N GLY M 349 " --> pdb=" O VAL M 375 " (cutoff:3.500A) 1246 hydrogen bonds defined for protein. 3663 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: 4.07 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.29: 3053 1.29 - 1.49: 11699 1.49 - 1.69: 9879 1.69 - 1.88: 126 1.88 - 2.08: 208 Bond restraints: 24965 Sorted by residual: bond pdb=" C VAL W 25 " pdb=" N HIS W 26 " ideal model delta sigma weight residual 1.335 1.432 -0.097 1.31e-02 5.83e+03 5.49e+01 bond pdb=" C1 PGV P 103 " pdb=" C2 PGV P 103 " ideal model delta sigma weight residual 1.504 1.365 0.139 2.00e-02 2.50e+03 4.82e+01 bond pdb=" C LEU C 295 " pdb=" N CYS C 296 " ideal model delta sigma weight residual 1.331 1.227 0.104 1.73e-02 3.34e+03 3.63e+01 bond pdb=" CAB KGD C 401 " pdb=" CAF KGD C 401 " ideal model delta sigma weight residual 1.536 1.417 0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" C VAL 4 25 " pdb=" N HIS 4 26 " ideal model delta sigma weight residual 1.335 1.415 -0.080 1.38e-02 5.25e+03 3.39e+01 ... (remaining 24960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 31385 3.37 - 6.73: 2652 6.73 - 10.10: 538 10.10 - 13.46: 178 13.46 - 16.83: 7 Bond angle restraints: 34760 Sorted by residual: angle pdb=" N ALA V 35 " pdb=" CA ALA V 35 " pdb=" C ALA V 35 " ideal model delta sigma weight residual 111.69 99.18 12.51 1.23e+00 6.61e-01 1.03e+02 angle pdb=" N GLY M 425 " pdb=" CA GLY M 425 " pdb=" C GLY M 425 " ideal model delta sigma weight residual 112.50 123.52 -11.02 1.16e+00 7.43e-01 9.03e+01 angle pdb=" N GLY L 307 " pdb=" CA GLY L 307 " pdb=" C GLY L 307 " ideal model delta sigma weight residual 113.37 123.41 -10.04 1.34e+00 5.57e-01 5.61e+01 angle pdb=" N PHE L 206 " pdb=" CA PHE L 206 " pdb=" C PHE L 206 " ideal model delta sigma weight residual 113.01 104.24 8.77 1.20e+00 6.94e-01 5.34e+01 angle pdb=" N THR L 97 " pdb=" CA THR L 97 " pdb=" C THR L 97 " ideal model delta sigma weight residual 111.36 119.32 -7.96 1.09e+00 8.42e-01 5.33e+01 ... (remaining 34755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.94: 12117 28.94 - 57.87: 880 57.87 - 86.81: 116 86.81 - 115.74: 24 115.74 - 144.68: 24 Dihedral angle restraints: 13161 sinusoidal: 6438 harmonic: 6723 Sorted by residual: dihedral pdb=" C1 BCL S 102 " pdb=" CGA BCL S 102 " pdb=" O2A BCL S 102 " pdb=" CBA BCL S 102 " ideal model delta sinusoidal sigma weight residual -180.00 -54.93 -125.07 1 6.00e+00 2.78e-02 4.20e+02 dihedral pdb=" C1 BCL F 102 " pdb=" CGA BCL F 102 " pdb=" O2A BCL F 102 " pdb=" CBA BCL F 102 " ideal model delta sinusoidal sigma weight residual -180.00 -54.97 -125.03 1 6.00e+00 2.78e-02 4.20e+02 dihedral pdb=" C1 BCL 8 101 " pdb=" CGA BCL 8 101 " pdb=" O2A BCL 8 101 " pdb=" CBA BCL 8 101 " ideal model delta sinusoidal sigma weight residual -180.00 -54.98 -125.02 1 6.00e+00 2.78e-02 4.20e+02 ... (remaining 13158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.118: 3408 1.118 - 2.236: 0 2.236 - 3.353: 0 3.353 - 4.471: 0 4.471 - 5.589: 16 Chirality restraints: 3424 Sorted by residual: chirality pdb=" C18 BCL X 101 " pdb=" C17 BCL X 101 " pdb=" C19 BCL X 101 " pdb=" C20 BCL X 101 " both_signs ideal model delta sigma weight residual False 2.71 -2.88 5.59 2.00e-01 2.50e+01 7.81e+02 chirality pdb=" C18 BCL W 102 " pdb=" C17 BCL W 102 " pdb=" C19 BCL W 102 " pdb=" C20 BCL W 102 " both_signs ideal model delta sigma weight residual False 2.71 -2.84 5.55 2.00e-01 2.50e+01 7.71e+02 chirality pdb=" C18 BCL 5 101 " pdb=" C17 BCL 5 101 " pdb=" C19 BCL 5 101 " pdb=" C20 BCL 5 101 " both_signs ideal model delta sigma weight residual False 2.71 -2.84 5.55 2.00e-01 2.50e+01 7.69e+02 ... (remaining 3421 not shown) Planarity restraints: 4222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL L1001 " 0.343 1.50e-02 4.44e+03 2.91e-01 1.88e+03 pdb=" C2 BCL L1001 " -0.400 1.50e-02 4.44e+03 pdb=" C3 BCL L1001 " -0.247 1.50e-02 4.44e+03 pdb=" C4 BCL L1001 " 0.016 1.50e-02 4.44e+03 pdb=" C5 BCL L1001 " 0.289 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C3D BCL L1001 " 0.051 5.00e-03 4.00e+04 9.26e-02 1.37e+03 pdb=" CAD BCL L1001 " -0.160 5.00e-03 4.00e+04 pdb=" CBD BCL L1001 " 0.043 5.00e-03 4.00e+04 pdb=" OBD BCL L1001 " 0.066 5.00e-03 4.00e+04 delta sigma weight rms_deltas residual plane pdb=" C3D BCL B 101 " 0.043 5.00e-03 4.00e+04 7.89e-02 9.96e+02 pdb=" CAD BCL B 101 " -0.136 5.00e-03 4.00e+04 pdb=" CBD BCL B 101 " 0.036 5.00e-03 4.00e+04 pdb=" OBD BCL B 101 " 0.056 5.00e-03 4.00e+04 ... (remaining 4219 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 96 2.44 - 3.06: 14798 3.06 - 3.67: 36960 3.67 - 4.29: 62204 4.29 - 4.90: 100285 Nonbonded interactions: 214343 Sorted by model distance: nonbonded pdb=" OE2 GLU M 557 " pdb="FE FE M 702 " model vdw 1.827 2.260 nonbonded pdb=" NE2 HIS L 229 " pdb="FE FE M 702 " model vdw 2.065 2.340 nonbonded pdb=" NE2 HIS C 122 " pdb="FE HEM C 402 " model vdw 2.105 3.080 nonbonded pdb=" O06 PGV P 103 " pdb=" O12 PGV P 103 " model vdw 2.109 3.040 nonbonded pdb=" NE2 HIS C 297 " pdb="FE HEM C 405 " model vdw 2.114 3.080 ... (remaining 214338 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 55) selection = (chain '2' and resid 7 through 55) selection = (chain '4' and resid 7 through 55) selection = (chain '6' and resid 7 through 55) selection = (chain '8' and resid 7 through 55) selection = (chain 'B' and resid 7 through 55) selection = (chain 'E' and resid 7 through 55) selection = (chain 'G' and resid 7 through 55) selection = (chain 'I' and resid 7 through 55) selection = (chain 'K' and resid 7 through 55) selection = (chain 'O' and resid 7 through 55) selection = (chain 'Q' and resid 7 through 55) selection = (chain 'S' and resid 7 through 55) selection = (chain 'U' and resid 7 through 55) selection = (chain 'W' and resid 7 through 55) } ncs_group { reference = (chain '1' and resid 7 through 41) selection = (chain '3' and resid 7 through 41) selection = (chain '5' and resid 7 through 41) selection = (chain '7' and resid 7 through 41) selection = (chain '9' and resid 7 through 41) selection = (chain 'A' and resid 7 through 41) selection = (chain 'D' and resid 7 through 41) selection = (chain 'F' and resid 7 through 41) selection = (chain 'H' and resid 7 through 41) selection = (chain 'J' and resid 7 through 41) selection = (chain 'N' and resid 7 through 41) selection = (chain 'P' and resid 7 through 41) selection = (chain 'R' and resid 7 through 41) selection = (chain 'T' and resid 7 through 41) selection = (chain 'V' and resid 7 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: 1.710 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: 0.260 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.760 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 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 : 0.029 0.659 25026 Z= 2.286 Angle : 2.080 16.829 34760 Z= 0.863 Chirality : 0.397 5.589 3424 Planarity : 0.031 0.293 4222 Dihedral : 20.784 144.679 8791 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 24.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.63 % Favored : 96.32 % Rotamer: Outliers : 0.66 % Allowed : 9.24 % Favored : 90.10 % Cbeta Deviations : 0.05 % 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: -0.29 (0.16), residues: 2256 helix: 0.58 (0.12), residues: 1410 sheet: None (None), residues: 0 loop : -1.47 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG V 40 TYR 0.018 0.002 TYR C 156 PHE 0.025 0.002 PHE L 206 TRP 0.031 0.002 TRP D 38 HIS 0.007 0.001 HIS M 589 Details of bonding type rmsd covalent geometry : bond 0.01966 (24965) covalent geometry : angle 2.07962 (34760) hydrogen bonds : bond 0.10891 ( 1246) hydrogen bonds : angle 5.24901 ( 3663) Misc. bond : bond 0.43468 ( 61) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 455 time to evaluate : 0.663 Fit side-chains REVERT: 0 19 ASN cc_start: 0.6837 (t0) cc_final: 0.6613 (t0) REVERT: 3 22 MET cc_start: 0.8708 (mmm) cc_final: 0.8483 (mmp) REVERT: 4 27 ASP cc_start: 0.7372 (t0) cc_final: 0.7171 (t70) REVERT: 9 17 LEU cc_start: 0.8112 (tp) cc_final: 0.7724 (mm) REVERT: A 22 MET cc_start: 0.9140 (mmm) cc_final: 0.8900 (mmp) REVERT: D 9 ARG cc_start: 0.6433 (ttp-170) cc_final: 0.5951 (tmt170) REVERT: D 10 THR cc_start: 0.8295 (m) cc_final: 0.8083 (m) REVERT: G 31 LYS cc_start: 0.8370 (mttt) cc_final: 0.8160 (mttp) REVERT: J 4 ARG cc_start: 0.6410 (tpt-90) cc_final: 0.6183 (mtp180) REVERT: L 151 ASP cc_start: 0.8847 (m-30) cc_final: 0.8552 (m-30) REVERT: N 9 ARG cc_start: 0.7503 (ttp-170) cc_final: 0.7278 (ttm170) REVERT: S 19 ASN cc_start: 0.7880 (t0) cc_final: 0.7634 (t0) REVERT: C 223 GLU cc_start: 0.8303 (tt0) cc_final: 0.7995 (tt0) REVERT: X 8 PHE cc_start: 0.6827 (t80) cc_final: 0.6595 (t80) REVERT: Z 43 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8190 (ttpp) outliers start: 13 outliers final: 6 residues processed: 466 average time/residue: 0.5334 time to fit residues: 289.0954 Evaluate side-chains 329 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 322 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 305 TRP Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain Z residue 39 ARG Chi-restraints excluded: chain Z residue 43 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 13 GLN ** 8 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN G 19 ASN I 19 ASN L 120 GLN M 572 GLN O 13 GLN Q 13 GLN S 22 GLN W 13 GLN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 GLN ** Z 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.118492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.100782 restraints weight = 31082.730| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.21 r_work: 0.2867 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.452 25026 Z= 0.180 Angle : 0.961 18.218 34760 Z= 0.345 Chirality : 0.041 0.215 3424 Planarity : 0.005 0.068 4222 Dihedral : 21.542 179.256 4800 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.49 % Allowed : 14.32 % Favored : 83.19 % 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: 1.51 (0.17), residues: 2256 helix: 2.11 (0.13), residues: 1419 sheet: None (None), residues: 0 loop : -1.00 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 9 40 TYR 0.013 0.002 TYR C 230 PHE 0.016 0.001 PHE C 39 TRP 0.015 0.001 TRP K 50 HIS 0.005 0.001 HIS M 589 Details of bonding type rmsd covalent geometry : bond 0.00458 (24965) covalent geometry : angle 0.96143 (34760) hydrogen bonds : bond 0.04545 ( 1246) hydrogen bonds : angle 4.18760 ( 3663) Misc. bond : bond 0.10778 ( 61) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 363 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: 0 9 LEU cc_start: 0.7946 (tp) cc_final: 0.7724 (mp) REVERT: 4 27 ASP cc_start: 0.7951 (t0) cc_final: 0.7631 (t70) REVERT: 6 17 LEU cc_start: 0.8105 (mt) cc_final: 0.7890 (mt) REVERT: 9 17 LEU cc_start: 0.8358 (tp) cc_final: 0.7859 (mp) REVERT: D 7 GLU cc_start: 0.7041 (tp30) cc_final: 0.6728 (mm-30) REVERT: D 9 ARG cc_start: 0.7068 (ttp-170) cc_final: 0.5970 (tmt170) REVERT: D 10 THR cc_start: 0.8459 (m) cc_final: 0.8176 (m) REVERT: E 31 LYS cc_start: 0.8520 (mttm) cc_final: 0.8253 (mtpp) REVERT: G 31 LYS cc_start: 0.8611 (mttt) cc_final: 0.8222 (mtpp) REVERT: K 27 ASP cc_start: 0.8235 (t0) cc_final: 0.8004 (t0) REVERT: L 41 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7576 (mt-10) REVERT: L 151 ASP cc_start: 0.9225 (m-30) cc_final: 0.8827 (m-30) REVERT: M 348 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7659 (mm-30) REVERT: N 9 ARG cc_start: 0.8078 (ttp-170) cc_final: 0.7757 (ttm170) REVERT: P 38 TRP cc_start: 0.8928 (OUTLIER) cc_final: 0.8629 (t60) REVERT: U 55 ARG cc_start: 0.7594 (mtm-85) cc_final: 0.7373 (mtm-85) REVERT: W 8 ASP cc_start: 0.7240 (p0) cc_final: 0.6710 (t0) REVERT: W 9 LEU cc_start: 0.8052 (mt) cc_final: 0.7720 (mp) REVERT: W 17 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7581 (mm) REVERT: C 28 SER cc_start: 0.8196 (p) cc_final: 0.7981 (m) REVERT: C 73 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7603 (mp0) REVERT: C 145 MET cc_start: 0.8510 (mmt) cc_final: 0.7720 (mmt) REVERT: C 223 GLU cc_start: 0.8805 (tt0) cc_final: 0.8458 (tt0) REVERT: C 253 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7580 (mt-10) REVERT: C 272 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7086 (mp0) REVERT: X 8 PHE cc_start: 0.6495 (t80) cc_final: 0.6291 (t80) REVERT: Z 43 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8533 (tttm) outliers start: 49 outliers final: 17 residues processed: 385 average time/residue: 0.5076 time to fit residues: 228.8681 Evaluate side-chains 345 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 322 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 ILE Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 15 SER Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 5 residue 21 VAL Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain I residue 8 ASP Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 281 CYS Chi-restraints excluded: chain L residue 285 SER Chi-restraints excluded: chain L residue 305 TRP Chi-restraints excluded: chain M residue 348 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 519 PHE Chi-restraints excluded: chain M residue 632 ASN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain P residue 38 TRP Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain Z residue 43 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 41 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 170 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 191 optimal weight: 0.6980 chunk 197 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 13 GLN 2 22 GLN 4 22 GLN 5 37 ASN ** 8 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN I 7 ASN I 19 ASN L 120 GLN M 369 GLN W 13 GLN C 56 ASN ** Z 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.117865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.100490 restraints weight = 31080.242| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.11 r_work: 0.2863 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.405 25026 Z= 0.157 Angle : 0.755 14.239 34760 Z= 0.305 Chirality : 0.040 0.189 3424 Planarity : 0.005 0.048 4222 Dihedral : 19.072 179.917 4792 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.54 % Allowed : 15.44 % Favored : 82.02 % 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: 1.95 (0.17), residues: 2256 helix: 2.44 (0.13), residues: 1438 sheet: None (None), residues: 0 loop : -0.87 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 4 TYR 0.013 0.002 TYR C 230 PHE 0.015 0.001 PHE L 185 TRP 0.016 0.001 TRP T 38 HIS 0.006 0.001 HIS M 589 Details of bonding type rmsd covalent geometry : bond 0.00384 (24965) covalent geometry : angle 0.75513 (34760) hydrogen bonds : bond 0.04251 ( 1246) hydrogen bonds : angle 3.91632 ( 3663) Misc. bond : bond 0.07528 ( 61) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 353 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: 0 27 ASP cc_start: 0.8555 (t70) cc_final: 0.8243 (t0) REVERT: 4 19 ASN cc_start: 0.7314 (t0) cc_final: 0.7082 (t0) REVERT: 4 27 ASP cc_start: 0.8105 (t0) cc_final: 0.7827 (t70) REVERT: 6 15 LYS cc_start: 0.8119 (mmtm) cc_final: 0.7901 (mmtm) REVERT: 6 17 LEU cc_start: 0.8133 (mt) cc_final: 0.7906 (mt) REVERT: 6 24 LEU cc_start: 0.8556 (mt) cc_final: 0.8328 (mt) REVERT: 8 20 ASN cc_start: 0.8425 (t0) cc_final: 0.7957 (m-40) REVERT: 9 17 LEU cc_start: 0.8444 (tp) cc_final: 0.7948 (mp) REVERT: 9 22 MET cc_start: 0.8985 (mmm) cc_final: 0.8743 (mmm) REVERT: D 9 ARG cc_start: 0.7070 (ttp-170) cc_final: 0.6086 (tmt170) REVERT: D 10 THR cc_start: 0.8475 (m) cc_final: 0.8200 (m) REVERT: F 9 ARG cc_start: 0.7716 (ttp-170) cc_final: 0.7390 (ttp80) REVERT: G 31 LYS cc_start: 0.8658 (mttt) cc_final: 0.8384 (mttp) REVERT: J 9 ARG cc_start: 0.8006 (ttp-110) cc_final: 0.7421 (ptt90) REVERT: L 151 ASP cc_start: 0.9197 (m-30) cc_final: 0.8821 (m-30) REVERT: M 348 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7634 (mm-30) REVERT: N 9 ARG cc_start: 0.7852 (ttp-170) cc_final: 0.7648 (ttm170) REVERT: P 9 ARG cc_start: 0.8524 (ttp-170) cc_final: 0.8120 (ttp-110) REVERT: Q 55 ARG cc_start: 0.7460 (ttm170) cc_final: 0.7205 (mtp180) REVERT: U 8 ASP cc_start: 0.7464 (p0) cc_final: 0.7154 (p0) REVERT: U 13 GLN cc_start: 0.8466 (tp40) cc_final: 0.8216 (tp40) REVERT: W 7 ASN cc_start: 0.6814 (p0) cc_final: 0.6452 (p0) REVERT: W 8 ASP cc_start: 0.7299 (p0) cc_final: 0.6819 (t0) REVERT: W 9 LEU cc_start: 0.8027 (mt) cc_final: 0.7798 (mp) REVERT: C 17 ARG cc_start: 0.7483 (tpt170) cc_final: 0.6419 (tpp80) REVERT: C 28 SER cc_start: 0.8197 (p) cc_final: 0.7963 (m) REVERT: C 188 GLU cc_start: 0.8244 (mp0) cc_final: 0.8026 (pt0) REVERT: C 223 GLU cc_start: 0.8814 (tt0) cc_final: 0.8454 (tt0) REVERT: C 272 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: X 25 MET cc_start: 0.6797 (OUTLIER) cc_final: 0.5806 (mpp) REVERT: X 26 SER cc_start: 0.6350 (OUTLIER) cc_final: 0.5849 (m) REVERT: Z 56 LYS cc_start: 0.7953 (mmtm) cc_final: 0.7592 (mmtt) outliers start: 50 outliers final: 20 residues processed: 385 average time/residue: 0.6156 time to fit residues: 275.5038 Evaluate side-chains 341 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 317 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 15 SER Chi-restraints excluded: chain 5 residue 21 VAL Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 285 SER Chi-restraints excluded: chain L residue 305 TRP Chi-restraints excluded: chain M residue 348 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 519 PHE Chi-restraints excluded: chain M residue 595 PHE Chi-restraints excluded: chain M residue 613 LEU Chi-restraints excluded: chain M residue 632 ASN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain Q residue 13 GLN Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain X residue 25 MET Chi-restraints excluded: chain X residue 26 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 168 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 202 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 160 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 108 optimal weight: 0.0870 chunk 174 optimal weight: 0.9980 overall best weight: 0.8158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 13 GLN 4 22 GLN ** 8 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN E 13 GLN I 19 ASN L 112 GLN L 120 GLN O 13 GLN W 13 GLN ** C 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN ** Z 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.120459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.103800 restraints weight = 31235.072| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.09 r_work: 0.2951 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.342 25026 Z= 0.132 Angle : 0.686 13.948 34760 Z= 0.282 Chirality : 0.038 0.215 3424 Planarity : 0.004 0.049 4222 Dihedral : 18.199 179.967 4788 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.34 % Allowed : 16.25 % Favored : 81.41 % 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: 2.23 (0.17), residues: 2256 helix: 2.66 (0.13), residues: 1439 sheet: None (None), residues: 0 loop : -0.76 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 8 55 TYR 0.012 0.001 TYR C 230 PHE 0.027 0.001 PHE X 8 TRP 0.014 0.001 TRP M 575 HIS 0.005 0.001 HIS M 589 Details of bonding type rmsd covalent geometry : bond 0.00312 (24965) covalent geometry : angle 0.68567 (34760) hydrogen bonds : bond 0.03981 ( 1246) hydrogen bonds : angle 3.77775 ( 3663) Misc. bond : bond 0.06482 ( 61) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 345 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: 0 9 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7709 (mp) REVERT: 0 27 ASP cc_start: 0.8549 (t70) cc_final: 0.8168 (t0) REVERT: 4 27 ASP cc_start: 0.8054 (t0) cc_final: 0.7789 (t70) REVERT: 6 17 LEU cc_start: 0.8080 (mt) cc_final: 0.7814 (mt) REVERT: 6 24 LEU cc_start: 0.8524 (mt) cc_final: 0.8294 (mt) REVERT: 8 20 ASN cc_start: 0.8387 (t0) cc_final: 0.7858 (m-40) REVERT: 9 17 LEU cc_start: 0.8422 (tp) cc_final: 0.8009 (mm) REVERT: 9 22 MET cc_start: 0.8998 (mmm) cc_final: 0.8707 (mmm) REVERT: B 9 LEU cc_start: 0.8155 (mm) cc_final: 0.7582 (mp) REVERT: B 31 LYS cc_start: 0.8870 (mttt) cc_final: 0.8605 (mmtp) REVERT: D 7 GLU cc_start: 0.7410 (tp30) cc_final: 0.6924 (mm-30) REVERT: D 9 ARG cc_start: 0.7050 (ttp-170) cc_final: 0.6079 (tmt170) REVERT: E 31 LYS cc_start: 0.8542 (mttm) cc_final: 0.8257 (mtpp) REVERT: F 9 ARG cc_start: 0.7605 (ttp-170) cc_final: 0.7342 (ttp80) REVERT: G 31 LYS cc_start: 0.8622 (mttt) cc_final: 0.8361 (mttp) REVERT: I 31 LYS cc_start: 0.8875 (mtpt) cc_final: 0.8572 (mtmm) REVERT: J 9 ARG cc_start: 0.7877 (ttp-110) cc_final: 0.7225 (ptt-90) REVERT: L 151 ASP cc_start: 0.9180 (m-30) cc_final: 0.8831 (m-30) REVERT: L 243 ASP cc_start: 0.7124 (t70) cc_final: 0.6907 (t0) REVERT: M 348 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7585 (mm-30) REVERT: P 9 ARG cc_start: 0.8480 (ttp-170) cc_final: 0.8094 (ttp-110) REVERT: Q 55 ARG cc_start: 0.7410 (ttm170) cc_final: 0.7174 (mtp180) REVERT: U 8 ASP cc_start: 0.7521 (p0) cc_final: 0.7289 (p0) REVERT: U 13 GLN cc_start: 0.8449 (tp40) cc_final: 0.8192 (tp40) REVERT: W 8 ASP cc_start: 0.7470 (p0) cc_final: 0.6928 (t0) REVERT: C 145 MET cc_start: 0.8623 (mmt) cc_final: 0.7599 (mmt) REVERT: C 223 GLU cc_start: 0.8764 (tt0) cc_final: 0.8397 (tt0) REVERT: C 272 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: X 26 SER cc_start: 0.6327 (OUTLIER) cc_final: 0.6050 (m) REVERT: Z 56 LYS cc_start: 0.7918 (mmtm) cc_final: 0.7545 (mmtt) outliers start: 46 outliers final: 21 residues processed: 367 average time/residue: 0.5397 time to fit residues: 232.7225 Evaluate side-chains 338 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 313 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 9 LEU Chi-restraints excluded: chain 3 residue 15 SER Chi-restraints excluded: chain 8 residue 31 LYS Chi-restraints excluded: chain 9 residue 10 THR Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain J residue 22 MET Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 285 SER Chi-restraints excluded: chain L residue 305 TRP Chi-restraints excluded: chain M residue 348 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 519 PHE Chi-restraints excluded: chain M residue 595 PHE Chi-restraints excluded: chain M residue 632 ASN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain Q residue 13 GLN Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Y residue 24 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 chunk 3 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 108 optimal weight: 0.0980 chunk 5 optimal weight: 7.9990 chunk 146 optimal weight: 0.9990 chunk 142 optimal weight: 10.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 13 GLN 4 22 GLN ** 8 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN E 13 GLN I 19 ASN L 120 GLN L 293 ASN O 13 GLN W 13 GLN ** Z 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.118695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.101364 restraints weight = 31124.929| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.12 r_work: 0.2930 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.345 25026 Z= 0.137 Angle : 0.687 13.858 34760 Z= 0.283 Chirality : 0.038 0.196 3424 Planarity : 0.004 0.053 4222 Dihedral : 17.745 179.951 4788 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.34 % Allowed : 16.15 % Favored : 81.51 % 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: 2.32 (0.17), residues: 2256 helix: 2.70 (0.13), residues: 1438 sheet: None (None), residues: 0 loop : -0.66 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 8 55 TYR 0.014 0.001 TYR C 230 PHE 0.024 0.001 PHE X 8 TRP 0.012 0.001 TRP W 50 HIS 0.006 0.001 HIS M 589 Details of bonding type rmsd covalent geometry : bond 0.00332 (24965) covalent geometry : angle 0.68728 (34760) hydrogen bonds : bond 0.04034 ( 1246) hydrogen bonds : angle 3.73555 ( 3663) Misc. bond : bond 0.06561 ( 61) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 328 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 9 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7680 (mp) REVERT: 0 27 ASP cc_start: 0.8533 (t70) cc_final: 0.8165 (t0) REVERT: 4 27 ASP cc_start: 0.7939 (t0) cc_final: 0.7686 (t70) REVERT: 6 17 LEU cc_start: 0.8233 (mt) cc_final: 0.7998 (mt) REVERT: 6 24 LEU cc_start: 0.8551 (mt) cc_final: 0.8331 (mt) REVERT: 7 9 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6796 (ttt-90) REVERT: 8 20 ASN cc_start: 0.8362 (t0) cc_final: 0.7878 (m-40) REVERT: 9 17 LEU cc_start: 0.8418 (tp) cc_final: 0.8019 (mm) REVERT: 9 22 MET cc_start: 0.9026 (mmm) cc_final: 0.8770 (mmm) REVERT: B 31 LYS cc_start: 0.8872 (mttt) cc_final: 0.8615 (mmtp) REVERT: D 7 GLU cc_start: 0.7404 (tp30) cc_final: 0.6913 (mm-30) REVERT: D 9 ARG cc_start: 0.7045 (ttp-170) cc_final: 0.6108 (tmt170) REVERT: E 31 LYS cc_start: 0.8553 (mttm) cc_final: 0.8310 (mtpp) REVERT: F 9 ARG cc_start: 0.7611 (ttp-170) cc_final: 0.7352 (ttp80) REVERT: G 31 LYS cc_start: 0.8605 (mttt) cc_final: 0.8368 (mttp) REVERT: L 151 ASP cc_start: 0.9160 (m-30) cc_final: 0.8823 (m-30) REVERT: L 245 ASN cc_start: 0.9011 (m110) cc_final: 0.8789 (m-40) REVERT: M 348 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7566 (mm-30) REVERT: Q 55 ARG cc_start: 0.7439 (ttm170) cc_final: 0.7212 (mtp180) REVERT: S 31 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8347 (mttt) REVERT: U 13 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8186 (tp40) REVERT: W 8 ASP cc_start: 0.7531 (p0) cc_final: 0.7006 (t0) REVERT: C 31 MET cc_start: 0.6918 (ttm) cc_final: 0.6699 (ttm) REVERT: C 106 MET cc_start: 0.8038 (ttm) cc_final: 0.7652 (ttm) REVERT: C 145 MET cc_start: 0.8616 (mmt) cc_final: 0.7631 (mmt) REVERT: C 223 GLU cc_start: 0.8774 (tt0) cc_final: 0.8371 (tt0) REVERT: C 272 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7574 (mp0) REVERT: Z 56 LYS cc_start: 0.7897 (mmtm) cc_final: 0.7511 (mmtt) outliers start: 46 outliers final: 22 residues processed: 357 average time/residue: 0.5046 time to fit residues: 212.7526 Evaluate side-chains 334 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 306 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 9 LEU Chi-restraints excluded: chain 3 residue 15 SER Chi-restraints excluded: chain 7 residue 9 ARG Chi-restraints excluded: chain 8 residue 31 LYS Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain J residue 22 MET Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 285 SER Chi-restraints excluded: chain L residue 305 TRP Chi-restraints excluded: chain M residue 348 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 430 VAL Chi-restraints excluded: chain M residue 519 PHE Chi-restraints excluded: chain M residue 595 PHE Chi-restraints excluded: chain M residue 632 ASN Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain S residue 31 LYS Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain U residue 13 GLN Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Z residue 47 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 38 optimal weight: 0.7980 chunk 183 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 162 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 13 GLN 4 22 GLN ** 8 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN E 13 GLN I 19 ASN L 120 GLN L 306 ASN O 13 GLN ** O 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 13 GLN ** Z 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.112335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.094731 restraints weight = 31408.130| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.19 r_work: 0.2806 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.442 25026 Z= 0.232 Angle : 0.844 16.731 34760 Z= 0.338 Chirality : 0.043 0.220 3424 Planarity : 0.005 0.055 4222 Dihedral : 18.094 179.825 4787 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.69 % Allowed : 16.10 % Favored : 81.21 % 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: 1.96 (0.17), residues: 2256 helix: 2.38 (0.13), residues: 1436 sheet: None (None), residues: 0 loop : -0.71 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 8 55 TYR 0.018 0.002 TYR M 424 PHE 0.024 0.002 PHE X 8 TRP 0.015 0.002 TRP T 38 HIS 0.008 0.001 HIS M 589 Details of bonding type rmsd covalent geometry : bond 0.00579 (24965) covalent geometry : angle 0.84360 (34760) hydrogen bonds : bond 0.04696 ( 1246) hydrogen bonds : angle 4.02160 ( 3663) Misc. bond : bond 0.07282 ( 61) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 307 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 9 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7754 (mp) REVERT: 0 27 ASP cc_start: 0.8579 (t70) cc_final: 0.8247 (t0) REVERT: 0 38 ILE cc_start: 0.8590 (mm) cc_final: 0.8257 (mt) REVERT: 3 9 ARG cc_start: 0.7481 (ttp-170) cc_final: 0.6684 (ttt90) REVERT: 6 17 LEU cc_start: 0.8335 (mt) cc_final: 0.8125 (mt) REVERT: 7 9 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6853 (ttt180) REVERT: 8 20 ASN cc_start: 0.8449 (t0) cc_final: 0.7993 (m-40) REVERT: 9 17 LEU cc_start: 0.8457 (tp) cc_final: 0.8054 (mm) REVERT: D 7 GLU cc_start: 0.7571 (tp30) cc_final: 0.6976 (mm-30) REVERT: D 9 ARG cc_start: 0.7456 (ttp-170) cc_final: 0.6854 (ttt-90) REVERT: F 9 ARG cc_start: 0.7795 (ttp-170) cc_final: 0.7215 (ttt-90) REVERT: G 31 LYS cc_start: 0.8672 (mttt) cc_final: 0.8468 (mttp) REVERT: I 31 LYS cc_start: 0.8893 (mtpt) cc_final: 0.8612 (mtmm) REVERT: J 22 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.7591 (mpm) REVERT: L 48 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.7869 (mttm) REVERT: L 151 ASP cc_start: 0.9195 (m-30) cc_final: 0.8912 (m-30) REVERT: L 181 TRP cc_start: 0.7166 (OUTLIER) cc_final: 0.5539 (t-100) REVERT: M 505 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8805 (pt) REVERT: Q 55 ARG cc_start: 0.7478 (ttm170) cc_final: 0.7247 (mtp180) REVERT: S 31 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8424 (mttt) REVERT: U 13 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8203 (tp40) REVERT: W 8 ASP cc_start: 0.7573 (p0) cc_final: 0.7106 (t0) REVERT: C 223 GLU cc_start: 0.8864 (tt0) cc_final: 0.8552 (tt0) REVERT: C 272 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.7665 (mp0) REVERT: Z 56 LYS cc_start: 0.7948 (mmtm) cc_final: 0.7688 (mmtt) outliers start: 53 outliers final: 21 residues processed: 341 average time/residue: 0.6216 time to fit residues: 246.9699 Evaluate side-chains 322 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 292 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 9 LEU Chi-restraints excluded: chain 3 residue 15 SER Chi-restraints excluded: chain 5 residue 21 VAL Chi-restraints excluded: chain 7 residue 9 ARG Chi-restraints excluded: chain 8 residue 31 LYS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain J residue 22 MET Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 48 LYS Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 285 SER Chi-restraints excluded: chain L residue 305 TRP Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 430 VAL Chi-restraints excluded: chain M residue 505 ILE Chi-restraints excluded: chain M residue 519 PHE Chi-restraints excluded: chain M residue 632 ASN Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain Q residue 13 GLN Chi-restraints excluded: chain S residue 31 LYS Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain U residue 13 GLN Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain Z residue 47 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 119 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 175 optimal weight: 7.9990 chunk 162 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 142 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 13 GLN 4 22 GLN ** 8 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN E 13 GLN I 19 ASN L 120 GLN O 13 GLN ** O 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 22 GLN W 13 GLN ** Z 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.117736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.100932 restraints weight = 31171.188| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.05 r_work: 0.2918 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.350 25026 Z= 0.132 Angle : 0.694 14.787 34760 Z= 0.284 Chirality : 0.038 0.168 3424 Planarity : 0.004 0.050 4222 Dihedral : 17.493 179.960 4787 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.93 % Allowed : 17.37 % Favored : 80.70 % 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: 2.25 (0.17), residues: 2256 helix: 2.64 (0.13), residues: 1438 sheet: None (None), residues: 0 loop : -0.66 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 8 55 TYR 0.014 0.001 TYR C 133 PHE 0.026 0.001 PHE X 8 TRP 0.012 0.001 TRP M 575 HIS 0.005 0.001 HIS M 589 Details of bonding type rmsd covalent geometry : bond 0.00317 (24965) covalent geometry : angle 0.69440 (34760) hydrogen bonds : bond 0.04001 ( 1246) hydrogen bonds : angle 3.78128 ( 3663) Misc. bond : bond 0.05598 ( 61) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 326 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: 0 9 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7817 (mp) REVERT: 0 27 ASP cc_start: 0.8472 (t70) cc_final: 0.8122 (t0) REVERT: 0 38 ILE cc_start: 0.8556 (mm) cc_final: 0.8233 (mt) REVERT: 3 9 ARG cc_start: 0.7419 (ttp-170) cc_final: 0.6613 (ttt90) REVERT: 7 9 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.6755 (ttt180) REVERT: 8 20 ASN cc_start: 0.8319 (t0) cc_final: 0.7843 (m-40) REVERT: 9 17 LEU cc_start: 0.8378 (tp) cc_final: 0.7985 (mm) REVERT: 9 22 MET cc_start: 0.8940 (mmm) cc_final: 0.8717 (mmm) REVERT: B 31 LYS cc_start: 0.8882 (mttt) cc_final: 0.8626 (mmtp) REVERT: D 7 GLU cc_start: 0.7484 (tp30) cc_final: 0.6903 (mm-30) REVERT: D 9 ARG cc_start: 0.7315 (ttp-170) cc_final: 0.6756 (ttt-90) REVERT: E 31 LYS cc_start: 0.8549 (mttm) cc_final: 0.8331 (mtpp) REVERT: F 9 ARG cc_start: 0.7673 (ttp-170) cc_final: 0.7463 (ttp80) REVERT: G 31 LYS cc_start: 0.8637 (mttt) cc_final: 0.8384 (mttp) REVERT: I 31 LYS cc_start: 0.8839 (mtpt) cc_final: 0.8542 (mtmm) REVERT: J 9 ARG cc_start: 0.8109 (ttp-110) cc_final: 0.7290 (ptt90) REVERT: L 151 ASP cc_start: 0.9122 (m-30) cc_final: 0.8827 (m-30) REVERT: L 243 ASP cc_start: 0.7374 (t70) cc_final: 0.7133 (t0) REVERT: M 505 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8755 (pt) REVERT: N 9 ARG cc_start: 0.7946 (ttm170) cc_final: 0.7683 (ttp-170) REVERT: P 9 ARG cc_start: 0.8411 (ttp-170) cc_final: 0.8195 (ttm110) REVERT: U 13 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8191 (tp40) REVERT: W 8 ASP cc_start: 0.7545 (p0) cc_final: 0.7101 (t0) REVERT: C 31 MET cc_start: 0.6869 (ttm) cc_final: 0.6422 (mmp) REVERT: C 145 MET cc_start: 0.8606 (mmt) cc_final: 0.7472 (mmt) REVERT: C 223 GLU cc_start: 0.8764 (tt0) cc_final: 0.8401 (tt0) REVERT: C 272 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: Z 56 LYS cc_start: 0.7924 (mmtm) cc_final: 0.7647 (mmtt) outliers start: 38 outliers final: 20 residues processed: 351 average time/residue: 0.5655 time to fit residues: 233.5920 Evaluate side-chains 327 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 302 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 9 LEU Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 7 residue 9 ARG Chi-restraints excluded: chain 8 residue 31 LYS Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain J residue 22 MET Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 285 SER Chi-restraints excluded: chain L residue 305 TRP Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 430 VAL Chi-restraints excluded: chain M residue 505 ILE Chi-restraints excluded: chain M residue 519 PHE Chi-restraints excluded: chain M residue 595 PHE Chi-restraints excluded: chain M residue 632 ASN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain Q residue 13 GLN Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain U residue 13 GLN Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain Z residue 47 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 118 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 115 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 176 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 181 optimal weight: 9.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 13 GLN 4 22 GLN ** 8 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN E 13 GLN I 19 ASN L 120 GLN O 13 GLN W 13 GLN ** Z 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.118641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.101578 restraints weight = 31002.918| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.09 r_work: 0.2902 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.371 25026 Z= 0.131 Angle : 0.686 13.824 34760 Z= 0.282 Chirality : 0.038 0.157 3424 Planarity : 0.004 0.055 4222 Dihedral : 17.178 179.979 4787 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.18 % Allowed : 17.37 % Favored : 80.45 % 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 (0.17), residues: 2256 helix: 2.72 (0.12), residues: 1437 sheet: None (None), residues: 0 loop : -0.60 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 8 55 TYR 0.013 0.001 TYR C 133 PHE 0.025 0.001 PHE X 8 TRP 0.011 0.001 TRP C 41 HIS 0.005 0.001 HIS M 589 Details of bonding type rmsd covalent geometry : bond 0.00316 (24965) covalent geometry : angle 0.68556 (34760) hydrogen bonds : bond 0.03996 ( 1246) hydrogen bonds : angle 3.71718 ( 3663) Misc. bond : bond 0.05685 ( 61) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 321 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: 0 9 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7810 (mp) REVERT: 0 27 ASP cc_start: 0.8511 (t70) cc_final: 0.8214 (t70) REVERT: 2 7 ASN cc_start: 0.6954 (p0) cc_final: 0.6312 (p0) REVERT: 3 9 ARG cc_start: 0.7411 (ttp-170) cc_final: 0.6830 (ttm110) REVERT: 4 27 ASP cc_start: 0.8074 (t70) cc_final: 0.7820 (t0) REVERT: 7 9 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6806 (ttt180) REVERT: 8 20 ASN cc_start: 0.8305 (t0) cc_final: 0.7883 (m-40) REVERT: 9 17 LEU cc_start: 0.8424 (tp) cc_final: 0.8063 (mm) REVERT: B 31 LYS cc_start: 0.8865 (mttt) cc_final: 0.8458 (mmtt) REVERT: D 9 ARG cc_start: 0.7392 (ttp-170) cc_final: 0.6919 (ttt-90) REVERT: F 7 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6721 (mp0) REVERT: F 9 ARG cc_start: 0.7727 (ttp-170) cc_final: 0.7520 (ttp80) REVERT: I 31 LYS cc_start: 0.8868 (mtpt) cc_final: 0.8609 (mtmm) REVERT: J 9 ARG cc_start: 0.8139 (ttp-110) cc_final: 0.7351 (ptt90) REVERT: L 151 ASP cc_start: 0.9154 (m-30) cc_final: 0.8871 (m-30) REVERT: L 243 ASP cc_start: 0.7254 (t70) cc_final: 0.7000 (t0) REVERT: M 505 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8759 (pt) REVERT: N 9 ARG cc_start: 0.7975 (ttm170) cc_final: 0.7743 (ttp-170) REVERT: P 9 ARG cc_start: 0.8439 (ttp-170) cc_final: 0.8152 (ttp-110) REVERT: S 27 ASP cc_start: 0.8718 (t70) cc_final: 0.8513 (t70) REVERT: S 31 LYS cc_start: 0.8685 (mtpt) cc_final: 0.8255 (mptt) REVERT: U 13 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8200 (tp40) REVERT: V 11 SER cc_start: 0.8757 (m) cc_final: 0.8337 (p) REVERT: W 8 ASP cc_start: 0.7510 (p0) cc_final: 0.7077 (t0) REVERT: C 28 SER cc_start: 0.8372 (p) cc_final: 0.8057 (m) REVERT: C 106 MET cc_start: 0.8002 (ttm) cc_final: 0.7656 (ttm) REVERT: C 145 MET cc_start: 0.8693 (mmt) cc_final: 0.7632 (mmt) REVERT: C 223 GLU cc_start: 0.8795 (tt0) cc_final: 0.8406 (tt0) REVERT: Z 56 LYS cc_start: 0.7907 (mmtm) cc_final: 0.7532 (mmtt) outliers start: 43 outliers final: 27 residues processed: 349 average time/residue: 0.5856 time to fit residues: 240.3953 Evaluate side-chains 340 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 309 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 9 LEU Chi-restraints excluded: chain 5 residue 13 VAL Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 21 VAL Chi-restraints excluded: chain 7 residue 9 ARG Chi-restraints excluded: chain 8 residue 31 LYS Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain J residue 22 MET Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 285 SER Chi-restraints excluded: chain L residue 305 TRP Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 430 VAL Chi-restraints excluded: chain M residue 505 ILE Chi-restraints excluded: chain M residue 519 PHE Chi-restraints excluded: chain M residue 538 LEU Chi-restraints excluded: chain M residue 595 PHE Chi-restraints excluded: chain M residue 632 ASN Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain U residue 13 GLN Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain Y residue 11 MET Chi-restraints excluded: chain Z residue 47 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 28 optimal weight: 0.3980 chunk 119 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 171 optimal weight: 5.9990 chunk 190 optimal weight: 0.0970 chunk 67 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 13 GLN 4 22 GLN ** 8 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN E 13 GLN L 120 GLN O 13 GLN W 13 GLN Y 2 ASN ** Z 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.121948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.104907 restraints weight = 30558.417| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.06 r_work: 0.2949 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.337 25026 Z= 0.118 Angle : 0.654 12.743 34760 Z= 0.274 Chirality : 0.037 0.149 3424 Planarity : 0.004 0.054 4222 Dihedral : 16.760 179.988 4787 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.52 % Allowed : 18.79 % Favored : 79.69 % 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: 2.41 (0.17), residues: 2256 helix: 2.75 (0.12), residues: 1466 sheet: None (None), residues: 0 loop : -0.70 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG 8 55 TYR 0.016 0.001 TYR C 133 PHE 0.026 0.001 PHE X 8 TRP 0.012 0.001 TRP M 594 HIS 0.005 0.001 HIS M 589 Details of bonding type rmsd covalent geometry : bond 0.00275 (24965) covalent geometry : angle 0.65377 (34760) hydrogen bonds : bond 0.03801 ( 1246) hydrogen bonds : angle 3.60544 ( 3663) Misc. bond : bond 0.04945 ( 61) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 332 time to evaluate : 0.729 Fit side-chains REVERT: 0 7 ASN cc_start: 0.6919 (p0) cc_final: 0.6112 (t0) REVERT: 0 9 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7803 (mp) REVERT: 0 27 ASP cc_start: 0.8458 (t70) cc_final: 0.8174 (t70) REVERT: 2 7 ASN cc_start: 0.6946 (p0) cc_final: 0.6294 (p0) REVERT: 3 9 ARG cc_start: 0.7289 (ttp-170) cc_final: 0.6668 (ttm110) REVERT: 4 27 ASP cc_start: 0.7997 (t70) cc_final: 0.7725 (t0) REVERT: 7 9 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6709 (ttt180) REVERT: 8 20 ASN cc_start: 0.8242 (t0) cc_final: 0.7728 (m-40) REVERT: 9 17 LEU cc_start: 0.8288 (tp) cc_final: 0.7956 (mm) REVERT: B 31 LYS cc_start: 0.8769 (mttt) cc_final: 0.8341 (mmtt) REVERT: D 9 ARG cc_start: 0.7274 (ttp-170) cc_final: 0.6445 (tmt170) REVERT: F 9 ARG cc_start: 0.7651 (ttp-170) cc_final: 0.7432 (ttp80) REVERT: I 31 LYS cc_start: 0.8831 (mtpt) cc_final: 0.8554 (mtmm) REVERT: K 13 GLN cc_start: 0.7649 (tt0) cc_final: 0.7406 (tt0) REVERT: L 151 ASP cc_start: 0.9111 (m-30) cc_final: 0.8859 (m-30) REVERT: L 243 ASP cc_start: 0.7295 (t70) cc_final: 0.7073 (t0) REVERT: M 505 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8694 (pt) REVERT: N 9 ARG cc_start: 0.7927 (ttm170) cc_final: 0.7706 (ttp-170) REVERT: P 9 ARG cc_start: 0.8333 (ttp-170) cc_final: 0.8023 (ttp-110) REVERT: S 27 ASP cc_start: 0.8650 (t70) cc_final: 0.8206 (t0) REVERT: U 13 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8140 (tp40) REVERT: V 11 SER cc_start: 0.8644 (m) cc_final: 0.8240 (p) REVERT: W 8 ASP cc_start: 0.7438 (p0) cc_final: 0.7028 (t0) REVERT: C 106 MET cc_start: 0.7920 (ttm) cc_final: 0.7529 (ttm) REVERT: C 145 MET cc_start: 0.8647 (mmt) cc_final: 0.7617 (mmt) REVERT: C 188 GLU cc_start: 0.7958 (pt0) cc_final: 0.7700 (mp0) REVERT: C 223 GLU cc_start: 0.8740 (tt0) cc_final: 0.8343 (tt0) REVERT: X 19 TYR cc_start: 0.6883 (t80) cc_final: 0.6417 (t80) REVERT: Z 56 LYS cc_start: 0.7859 (mmtm) cc_final: 0.7487 (mmtt) outliers start: 30 outliers final: 20 residues processed: 352 average time/residue: 0.4745 time to fit residues: 197.9448 Evaluate side-chains 336 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 312 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 9 LEU Chi-restraints excluded: chain 5 residue 13 VAL Chi-restraints excluded: chain 5 residue 21 VAL Chi-restraints excluded: chain 7 residue 9 ARG Chi-restraints excluded: chain 8 residue 31 LYS Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 285 SER Chi-restraints excluded: chain L residue 305 TRP Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 505 ILE Chi-restraints excluded: chain M residue 538 LEU Chi-restraints excluded: chain M residue 595 PHE Chi-restraints excluded: chain M residue 632 ASN Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain U residue 13 GLN Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain Y residue 11 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 127 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 146 optimal weight: 8.9990 chunk 132 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 13 GLN 4 22 GLN ** 8 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN H 37 ASN L 120 GLN L 306 ASN O 13 GLN ** O 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 ASN S 22 GLN U 7 ASN W 13 GLN Y 2 ASN ** Z 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.116522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.099548 restraints weight = 30770.663| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.06 r_work: 0.2849 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.446 25026 Z= 0.163 Angle : 0.728 14.554 34760 Z= 0.300 Chirality : 0.039 0.171 3424 Planarity : 0.004 0.058 4222 Dihedral : 16.935 179.962 4787 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.68 % Allowed : 19.25 % Favored : 79.08 % 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: 2.38 (0.17), residues: 2256 helix: 2.72 (0.12), residues: 1437 sheet: None (None), residues: 0 loop : -0.57 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG 8 55 TYR 0.016 0.002 TYR C 133 PHE 0.025 0.001 PHE X 8 TRP 0.015 0.001 TRP C 41 HIS 0.006 0.001 HIS M 589 Details of bonding type rmsd covalent geometry : bond 0.00402 (24965) covalent geometry : angle 0.72822 (34760) hydrogen bonds : bond 0.04170 ( 1246) hydrogen bonds : angle 3.75284 ( 3663) Misc. bond : bond 0.06723 ( 61) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 316 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 9 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7816 (mp) REVERT: 0 27 ASP cc_start: 0.8538 (t70) cc_final: 0.8318 (t70) REVERT: 2 7 ASN cc_start: 0.7010 (p0) cc_final: 0.6364 (p0) REVERT: 3 9 ARG cc_start: 0.7350 (ttp-170) cc_final: 0.6755 (ttm110) REVERT: 7 9 ARG cc_start: 0.7075 (OUTLIER) cc_final: 0.6714 (ttt180) REVERT: 8 20 ASN cc_start: 0.8284 (t0) cc_final: 0.7854 (m-40) REVERT: 9 17 LEU cc_start: 0.8290 (tp) cc_final: 0.7962 (mm) REVERT: D 9 ARG cc_start: 0.7372 (ttp-170) cc_final: 0.6851 (ttt-90) REVERT: F 9 ARG cc_start: 0.7711 (ttp-170) cc_final: 0.7471 (ttp80) REVERT: J 9 ARG cc_start: 0.8165 (ttp-110) cc_final: 0.7350 (ptt90) REVERT: K 13 GLN cc_start: 0.7779 (tt0) cc_final: 0.7510 (tt0) REVERT: L 151 ASP cc_start: 0.9140 (m-30) cc_final: 0.8875 (m-30) REVERT: L 243 ASP cc_start: 0.7465 (t70) cc_final: 0.7253 (t0) REVERT: M 505 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8754 (pt) REVERT: N 9 ARG cc_start: 0.7971 (ttm170) cc_final: 0.7733 (ttp-170) REVERT: P 9 ARG cc_start: 0.8466 (ttp-170) cc_final: 0.8159 (ttp-110) REVERT: S 31 LYS cc_start: 0.8719 (mtpt) cc_final: 0.8402 (mptt) REVERT: U 13 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8181 (tp40) REVERT: V 11 SER cc_start: 0.8659 (m) cc_final: 0.8285 (p) REVERT: C 106 MET cc_start: 0.7975 (ttm) cc_final: 0.7628 (ttm) REVERT: C 223 GLU cc_start: 0.8815 (tt0) cc_final: 0.8474 (tt0) REVERT: X 19 TYR cc_start: 0.6888 (t80) cc_final: 0.6474 (t80) REVERT: Z 56 LYS cc_start: 0.7896 (mmtm) cc_final: 0.7644 (mmtt) outliers start: 33 outliers final: 25 residues processed: 340 average time/residue: 0.4954 time to fit residues: 198.0678 Evaluate side-chains 335 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 306 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 9 LEU Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 5 residue 13 VAL Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 21 VAL Chi-restraints excluded: chain 7 residue 9 ARG Chi-restraints excluded: chain 8 residue 31 LYS Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 285 SER Chi-restraints excluded: chain L residue 305 TRP Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 430 VAL Chi-restraints excluded: chain M residue 505 ILE Chi-restraints excluded: chain M residue 538 LEU Chi-restraints excluded: chain M residue 595 PHE Chi-restraints excluded: chain M residue 632 ASN Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain U residue 13 GLN Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain Y residue 11 MET Chi-restraints excluded: chain Y residue 24 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 151 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 199 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 13 GLN 4 22 GLN ** 8 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN H 37 ASN L 120 GLN O 13 GLN ** O 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 22 GLN U 7 ASN W 13 GLN Y 2 ASN ** Z 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.118286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.100775 restraints weight = 30609.323| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.11 r_work: 0.2877 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.428 25026 Z= 0.144 Angle : 0.706 13.948 34760 Z= 0.291 Chirality : 0.038 0.164 3424 Planarity : 0.004 0.055 4222 Dihedral : 16.826 179.977 4787 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.98 % Allowed : 18.74 % Favored : 79.28 % 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: 2.39 (0.17), residues: 2256 helix: 2.73 (0.12), residues: 1438 sheet: None (None), residues: 0 loop : -0.58 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG 8 55 TYR 0.018 0.002 TYR U 34 PHE 0.025 0.001 PHE X 8 TRP 0.021 0.001 TRP C 41 HIS 0.006 0.001 HIS M 589 Details of bonding type rmsd covalent geometry : bond 0.00351 (24965) covalent geometry : angle 0.70580 (34760) hydrogen bonds : bond 0.04077 ( 1246) hydrogen bonds : angle 3.73986 ( 3663) Misc. bond : bond 0.06488 ( 61) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7471.47 seconds wall clock time: 128 minutes 5.16 seconds (7685.16 seconds total)