Starting phenix.real_space_refine on Sun Jun 22 00:07:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hju_34838/06_2025/8hju_34838.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hju_34838/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hju_34838/06_2025/8hju_34838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hju_34838/06_2025/8hju_34838.map" model { file = "/net/cci-nas-00/data/ceres_data/8hju_34838/06_2025/8hju_34838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hju_34838/06_2025/8hju_34838.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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-12': 1, 'MQE:plan-11': 1, 'MQE:plan-10': 1, 'PGV:plan-3': 1, 'MQE:plan-9': 1, 'MQE:plan-6': 1, 'MQE:plan-5': 1, 'MQE:plan-4': 1, 'MQE:plan-3': 1, 'MQE:plan-2': 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: 15.32, per 1000 atoms: 0.64 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: 7.35 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.62 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: 6.08 Time building geometry restraints manager: 8.40 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 50.790 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.900 ------------------------------------------------------------------------------- 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 : 25.04 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (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 TRP 0.031 0.002 TRP D 38 HIS 0.007 0.001 HIS M 589 PHE 0.025 0.002 PHE L 206 TYR 0.018 0.002 TYR C 156 ARG 0.004 0.000 ARG V 40 Details of bonding type rmsd hydrogen bonds : bond 0.10891 ( 1246) hydrogen bonds : angle 5.24901 ( 3663) covalent geometry : bond 0.01966 (24965) covalent geometry : angle 2.07962 (34760) 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 : 2.357 Fit side-chains REVERT: 0 19 ASN cc_start: 0.6837 (t0) cc_final: 0.6614 (t0) REVERT: 3 22 MET cc_start: 0.8708 (mmm) cc_final: 0.8482 (mmp) REVERT: 9 17 LEU cc_start: 0.8112 (tp) cc_final: 0.7725 (mm) REVERT: A 22 MET cc_start: 0.9140 (mmm) cc_final: 0.8901 (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: 0.8082 (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: 0.8551 (m-30) REVERT: N 9 ARG cc_start: 0.7503 (ttp-170) cc_final: 0.7282 (ttm170) REVERT: S 19 ASN cc_start: 0.7880 (t0) cc_final: 0.7636 (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: 1.5459 time to fit residues: 835.7912 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 : 6.098 ------------------------------------------------------------------------------- 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 173 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 369 GLN M 572 GLN O 13 GLN Q 13 GLN S 22 GLN W 13 GLN C 56 ASN C 87 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.119351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.101571 restraints weight = 31010.685| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.21 r_work: 0.2885 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.435 25026 Z= 0.168 Angle : 0.946 17.959 34760 Z= 0.341 Chirality : 0.041 0.208 3424 Planarity : 0.005 0.066 4222 Dihedral : 21.625 178.696 4800 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.74 % Allowed : 14.02 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.17), residues: 2256 helix: 2.14 (0.13), residues: 1419 sheet: None (None), residues: 0 loop : -0.98 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 50 HIS 0.005 0.001 HIS M 589 PHE 0.016 0.001 PHE C 39 TYR 0.013 0.002 TYR C 230 ARG 0.005 0.000 ARG 8 55 Details of bonding type rmsd hydrogen bonds : bond 0.04407 ( 1246) hydrogen bonds : angle 4.15759 ( 3663) covalent geometry : bond 0.00428 (24965) covalent geometry : angle 0.94606 (34760) Misc. bond : bond 0.10710 ( 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 417 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 363 time to evaluate : 2.617 Fit side-chains revert: symmetry clash REVERT: 0 9 LEU cc_start: 0.7960 (tp) cc_final: 0.7746 (mp) REVERT: 4 19 ASN cc_start: 0.7369 (t0) cc_final: 0.7087 (t0) REVERT: 6 17 LEU cc_start: 0.8113 (mt) cc_final: 0.7900 (mt) REVERT: 9 17 LEU cc_start: 0.8364 (tp) cc_final: 0.7877 (mp) REVERT: D 7 GLU cc_start: 0.7015 (tp30) cc_final: 0.6714 (mm-30) REVERT: D 9 ARG cc_start: 0.7084 (ttp-170) cc_final: 0.6000 (tmt170) REVERT: D 10 THR cc_start: 0.8462 (m) cc_final: 0.8189 (m) REVERT: E 31 LYS cc_start: 0.8531 (mttm) cc_final: 0.8279 (mtpp) REVERT: G 31 LYS cc_start: 0.8625 (mttt) cc_final: 0.8242 (mtpp) REVERT: K 27 ASP cc_start: 0.8251 (t0) cc_final: 0.8020 (t0) REVERT: L 41 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7599 (mt-10) REVERT: L 151 ASP cc_start: 0.9216 (m-30) cc_final: 0.8836 (m-30) REVERT: M 348 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7692 (mm-30) REVERT: N 9 ARG cc_start: 0.8026 (ttp-170) cc_final: 0.7597 (ttm170) REVERT: P 38 TRP cc_start: 0.8923 (OUTLIER) cc_final: 0.8636 (t60) REVERT: R 9 ARG cc_start: 0.8642 (tmm160) cc_final: 0.8412 (tmm160) REVERT: U 55 ARG cc_start: 0.7587 (mtm-85) cc_final: 0.7343 (mtm-85) REVERT: W 8 ASP cc_start: 0.7211 (p0) cc_final: 0.6689 (t0) REVERT: W 9 LEU cc_start: 0.8039 (mt) cc_final: 0.7720 (mp) REVERT: W 17 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7627 (mm) REVERT: C 28 SER cc_start: 0.8227 (p) cc_final: 0.8011 (m) REVERT: C 73 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7627 (mp0) REVERT: C 145 MET cc_start: 0.8538 (mmt) cc_final: 0.7761 (mmt) REVERT: C 188 GLU cc_start: 0.8264 (mp0) cc_final: 0.8039 (pt0) REVERT: C 223 GLU cc_start: 0.8802 (tt0) cc_final: 0.8460 (tt0) REVERT: C 272 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7135 (mp0) REVERT: Z 39 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8260 (tmt-80) REVERT: Z 43 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8498 (tttm) outliers start: 54 outliers final: 19 residues processed: 387 average time/residue: 1.1988 time to fit residues: 546.7734 Evaluate side-chains 346 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 320 time to evaluate : 2.208 ------------------------------------------------------------------------------- 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 10 THR Chi-restraints excluded: chain 5 residue 21 VAL Chi-restraints excluded: chain 7 residue 20 LEU 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 39 ARG 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 12 optimal weight: 10.0000 chunk 184 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 163 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 170 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- 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 ** O 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 7 ASN W 13 GLN C 126 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 = 0.3258 r_free = 0.3258 target = 0.114361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.096719 restraints weight = 31094.958| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.22 r_work: 0.2836 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.439 25026 Z= 0.209 Angle : 0.844 15.619 34760 Z= 0.334 Chirality : 0.042 0.228 3424 Planarity : 0.005 0.062 4222 Dihedral : 19.187 179.964 4796 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.35 % Allowed : 14.73 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.17), residues: 2256 helix: 2.25 (0.13), residues: 1436 sheet: None (None), residues: 0 loop : -0.92 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP T 38 HIS 0.008 0.001 HIS M 589 PHE 0.027 0.002 PHE X 8 TYR 0.016 0.002 TYR C 230 ARG 0.007 0.001 ARG H 4 Details of bonding type rmsd hydrogen bonds : bond 0.04658 ( 1246) hydrogen bonds : angle 4.04871 ( 3663) covalent geometry : bond 0.00522 (24965) covalent geometry : angle 0.84363 (34760) Misc. bond : bond 0.08265 ( 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 399 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 333 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 27 ASP cc_start: 0.8658 (t70) cc_final: 0.8314 (t0) REVERT: 4 19 ASN cc_start: 0.7351 (t0) cc_final: 0.7151 (t0) REVERT: 6 17 LEU cc_start: 0.8208 (mt) cc_final: 0.7950 (mt) REVERT: 6 24 LEU cc_start: 0.8564 (mt) cc_final: 0.8363 (mt) REVERT: 8 20 ASN cc_start: 0.8494 (OUTLIER) cc_final: 0.8092 (m-40) REVERT: 9 17 LEU cc_start: 0.8469 (tp) cc_final: 0.7993 (mp) REVERT: D 9 ARG cc_start: 0.7306 (ttp-170) cc_final: 0.6295 (tmt170) REVERT: D 10 THR cc_start: 0.8533 (m) cc_final: 0.8260 (m) REVERT: F 9 ARG cc_start: 0.7795 (ttp-170) cc_final: 0.7479 (ttp80) REVERT: G 31 LYS cc_start: 0.8708 (mttt) cc_final: 0.8493 (mttp) REVERT: J 9 ARG cc_start: 0.8167 (ttp-110) cc_final: 0.7592 (ptt90) REVERT: K 31 LYS cc_start: 0.9036 (mttt) cc_final: 0.8804 (mttp) REVERT: L 48 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8268 (mtpt) REVERT: L 151 ASP cc_start: 0.9230 (m-30) cc_final: 0.8865 (m-30) REVERT: L 181 TRP cc_start: 0.7019 (OUTLIER) cc_final: 0.5398 (t-100) REVERT: M 348 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7814 (mm-30) REVERT: N 9 ARG cc_start: 0.8091 (ttp-170) cc_final: 0.7649 (ttm170) REVERT: P 9 ARG cc_start: 0.8548 (ttp-170) cc_final: 0.8145 (ttp-110) REVERT: P 38 TRP cc_start: 0.8999 (OUTLIER) cc_final: 0.8657 (t60) REVERT: Q 55 ARG cc_start: 0.7621 (ttm170) cc_final: 0.7341 (mtp180) REVERT: U 8 ASP cc_start: 0.7525 (p0) cc_final: 0.7197 (p0) REVERT: U 13 GLN cc_start: 0.8471 (tp40) cc_final: 0.8222 (tp40) REVERT: W 7 ASN cc_start: 0.6608 (p0) cc_final: 0.6242 (p0) REVERT: W 8 ASP cc_start: 0.7354 (p0) cc_final: 0.6950 (t0) REVERT: W 9 LEU cc_start: 0.8015 (mt) cc_final: 0.7771 (mp) REVERT: C 17 ARG cc_start: 0.7579 (tpt170) cc_final: 0.6473 (tpp80) REVERT: C 28 SER cc_start: 0.8263 (p) cc_final: 0.8025 (m) REVERT: C 31 MET cc_start: 0.7166 (ttm) cc_final: 0.6753 (ttt) REVERT: C 145 MET cc_start: 0.8647 (mmt) cc_final: 0.7745 (mmt) REVERT: C 188 GLU cc_start: 0.8282 (mp0) cc_final: 0.8070 (pt0) REVERT: C 223 GLU cc_start: 0.8814 (tt0) cc_final: 0.8491 (tt0) REVERT: C 272 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: X 25 MET cc_start: 0.6931 (OUTLIER) cc_final: 0.5902 (mpp) REVERT: X 26 SER cc_start: 0.6360 (OUTLIER) cc_final: 0.5728 (p) REVERT: Z 43 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8524 (tttp) REVERT: Z 56 LYS cc_start: 0.7949 (mmtm) cc_final: 0.7665 (mmtt) outliers start: 66 outliers final: 28 residues processed: 372 average time/residue: 1.2222 time to fit residues: 531.1383 Evaluate side-chains 341 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 304 time to evaluate : 2.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 8 residue 20 ASN Chi-restraints excluded: chain 8 residue 31 LYS Chi-restraints excluded: chain 8 residue 32 THR Chi-restraints excluded: chain 9 residue 10 THR Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain I residue 37 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 345 ASP 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 11 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain P residue 38 TRP Chi-restraints excluded: chain Q residue 13 GLN Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain C residue 98 THR 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 Chi-restraints excluded: chain Z residue 43 LYS Chi-restraints excluded: chain Z residue 47 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 7 optimal weight: 9.9990 chunk 186 optimal weight: 4.9990 chunk 194 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 193 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 173 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 I 19 ASN L 120 GLN O 13 GLN S 22 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 = 0.3291 r_free = 0.3291 target = 0.116908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.099939 restraints weight = 31353.634| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.05 r_work: 0.2915 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.377 25026 Z= 0.149 Angle : 0.732 15.157 34760 Z= 0.295 Chirality : 0.039 0.222 3424 Planarity : 0.004 0.049 4222 Dihedral : 18.517 179.918 4792 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.39 % Allowed : 16.35 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.17), residues: 2256 helix: 2.52 (0.13), residues: 1436 sheet: None (None), residues: 0 loop : -0.85 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 575 HIS 0.006 0.001 HIS M 589 PHE 0.023 0.001 PHE X 8 TYR 0.013 0.002 TYR C 230 ARG 0.007 0.000 ARG 8 55 Details of bonding type rmsd hydrogen bonds : bond 0.04196 ( 1246) hydrogen bonds : angle 3.89122 ( 3663) covalent geometry : bond 0.00362 (24965) covalent geometry : angle 0.73220 (34760) Misc. bond : bond 0.07275 ( 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 383 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 336 time to evaluate : 4.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 9 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7670 (mp) REVERT: 0 27 ASP cc_start: 0.8472 (t70) cc_final: 0.8230 (t0) REVERT: 6 17 LEU cc_start: 0.8276 (mt) cc_final: 0.8001 (mt) REVERT: 7 9 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6788 (ttt180) REVERT: 8 20 ASN cc_start: 0.8430 (t0) cc_final: 0.7994 (m-40) REVERT: 9 17 LEU cc_start: 0.8435 (tp) cc_final: 0.7934 (mp) REVERT: B 31 LYS cc_start: 0.8854 (mttt) cc_final: 0.8591 (mmtp) REVERT: D 7 GLU cc_start: 0.7463 (tp30) cc_final: 0.6875 (mm-30) REVERT: D 9 ARG cc_start: 0.7160 (ttp-170) cc_final: 0.6211 (tmt170) REVERT: D 10 THR cc_start: 0.8410 (m) cc_final: 0.8140 (m) REVERT: F 9 ARG cc_start: 0.7658 (ttp-170) cc_final: 0.7395 (ttp80) REVERT: G 31 LYS cc_start: 0.8636 (mttt) cc_final: 0.8419 (mttp) REVERT: K 31 LYS cc_start: 0.8952 (mttt) cc_final: 0.8737 (mttp) REVERT: L 151 ASP cc_start: 0.9186 (m-30) cc_final: 0.8839 (m-30) REVERT: L 243 ASP cc_start: 0.7173 (t70) cc_final: 0.6930 (t0) REVERT: M 348 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7540 (mm-30) REVERT: N 9 ARG cc_start: 0.7872 (ttp-170) cc_final: 0.7427 (ttm170) REVERT: P 9 ARG cc_start: 0.8472 (ttp-170) cc_final: 0.8076 (ttp-110) REVERT: Q 55 ARG cc_start: 0.7523 (ttm170) cc_final: 0.7277 (mtp180) REVERT: S 31 LYS cc_start: 0.8661 (mttt) cc_final: 0.8447 (mppt) REVERT: U 8 ASP cc_start: 0.7509 (p0) cc_final: 0.7190 (p0) REVERT: U 13 GLN cc_start: 0.8427 (tp40) cc_final: 0.8175 (tp40) REVERT: W 7 ASN cc_start: 0.6563 (p0) cc_final: 0.6345 (p0) REVERT: W 8 ASP cc_start: 0.7515 (p0) cc_final: 0.7022 (t0) REVERT: C 31 MET cc_start: 0.6974 (ttm) cc_final: 0.6743 (ttm) REVERT: C 145 MET cc_start: 0.8569 (mmt) cc_final: 0.7552 (mmt) REVERT: C 202 GLU cc_start: 0.8136 (pm20) cc_final: 0.7913 (pm20) REVERT: C 223 GLU cc_start: 0.8763 (tt0) cc_final: 0.8383 (tt0) REVERT: C 272 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.7551 (mp0) REVERT: X 26 SER cc_start: 0.6308 (OUTLIER) cc_final: 0.5600 (p) REVERT: Z 43 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8374 (tttm) outliers start: 47 outliers final: 22 residues processed: 361 average time/residue: 1.9571 time to fit residues: 842.1273 Evaluate side-chains 332 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 304 time to evaluate : 3.345 ------------------------------------------------------------------------------- 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 G residue 37 LEU Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain J residue 22 MET 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 345 ASP 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 272 GLU Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Z residue 43 LYS Chi-restraints excluded: chain Z residue 47 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 0.3980 chunk 101 optimal weight: 0.0070 chunk 189 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 15 optimal weight: 0.0470 chunk 76 optimal weight: 0.7980 chunk 43 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 144 optimal weight: 0.7980 chunk 172 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- 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 S 22 GLN W 13 GLN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3354 r_free = 0.3354 target = 0.121538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.104490 restraints weight = 31138.387| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.14 r_work: 0.2959 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.323 25026 Z= 0.117 Angle : 0.659 14.098 34760 Z= 0.273 Chirality : 0.037 0.185 3424 Planarity : 0.004 0.051 4222 Dihedral : 17.927 179.992 4791 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.39 % Allowed : 16.15 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.17), residues: 2256 helix: 2.76 (0.13), residues: 1435 sheet: None (None), residues: 0 loop : -0.73 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 575 HIS 0.004 0.001 HIS M 589 PHE 0.024 0.001 PHE X 8 TYR 0.012 0.001 TYR X 19 ARG 0.009 0.000 ARG 8 55 Details of bonding type rmsd hydrogen bonds : bond 0.03869 ( 1246) hydrogen bonds : angle 3.69476 ( 3663) covalent geometry : bond 0.00272 (24965) covalent geometry : angle 0.65916 (34760) Misc. bond : bond 0.05899 ( 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 396 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 349 time to evaluate : 2.437 Fit side-chains revert: symmetry clash REVERT: 0 27 ASP cc_start: 0.8504 (t70) cc_final: 0.8184 (t0) REVERT: 3 9 ARG cc_start: 0.7403 (ttp-170) cc_final: 0.6610 (ttt90) REVERT: 4 27 ASP cc_start: 0.8058 (t70) cc_final: 0.7820 (t0) REVERT: 6 17 LEU cc_start: 0.8249 (mt) cc_final: 0.8040 (mt) REVERT: 7 9 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6842 (ttt-90) REVERT: 8 20 ASN cc_start: 0.8319 (t0) cc_final: 0.7896 (m-40) REVERT: 9 17 LEU cc_start: 0.8417 (tp) cc_final: 0.7967 (mp) REVERT: B 31 LYS cc_start: 0.8863 (mttt) cc_final: 0.8598 (mmtp) REVERT: D 7 GLU cc_start: 0.7484 (tp30) cc_final: 0.6961 (mm-30) REVERT: D 9 ARG cc_start: 0.7152 (ttp-170) cc_final: 0.6272 (tmt170) REVERT: G 31 LYS cc_start: 0.8622 (mttt) cc_final: 0.8400 (mttp) REVERT: J 9 ARG cc_start: 0.8088 (ttp-110) cc_final: 0.7321 (ptt90) REVERT: L 151 ASP cc_start: 0.9140 (m-30) cc_final: 0.8833 (m-30) REVERT: L 243 ASP cc_start: 0.7209 (t70) cc_final: 0.6998 (t0) REVERT: L 245 ASN cc_start: 0.8992 (m110) cc_final: 0.8760 (m-40) REVERT: M 348 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7526 (mm-30) REVERT: M 505 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8760 (pt) REVERT: M 595 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8110 (t80) REVERT: P 9 ARG cc_start: 0.8398 (ttp-170) cc_final: 0.8079 (ttp-110) REVERT: Q 55 ARG cc_start: 0.7528 (ttm170) cc_final: 0.7310 (mtp180) REVERT: U 13 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8132 (tp40) REVERT: V 7 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6547 (tt0) REVERT: V 11 SER cc_start: 0.8879 (OUTLIER) cc_final: 0.8348 (p) REVERT: W 7 ASN cc_start: 0.6828 (p0) cc_final: 0.6567 (p0) REVERT: W 8 ASP cc_start: 0.7554 (p0) cc_final: 0.7079 (t0) REVERT: C 106 MET cc_start: 0.8010 (ttm) cc_final: 0.7631 (ttm) REVERT: C 145 MET cc_start: 0.8644 (mmt) cc_final: 0.7638 (mmt) REVERT: C 223 GLU cc_start: 0.8745 (tt0) cc_final: 0.8367 (tt0) REVERT: C 272 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: X 26 SER cc_start: 0.6314 (OUTLIER) cc_final: 0.6081 (m) REVERT: Z 43 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8438 (tttp) REVERT: Z 56 LYS cc_start: 0.7873 (mmtm) cc_final: 0.7498 (mmtt) outliers start: 47 outliers final: 11 residues processed: 378 average time/residue: 1.3206 time to fit residues: 591.3896 Evaluate side-chains 325 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 304 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 T residue 12 VAL Chi-restraints excluded: chain U residue 13 GLN Chi-restraints excluded: chain V residue 7 GLU Chi-restraints excluded: chain V residue 11 SER Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Z residue 43 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 195 optimal weight: 6.9990 chunk 187 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 172 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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 227 HIS L 293 ASN L 306 ASN O 13 GLN ** O 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 22 GLN U 7 ASN W 13 GLN ** Z 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.113805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.096254 restraints weight = 31211.573| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.06 r_work: 0.2853 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.497 25026 Z= 0.208 Angle : 0.803 15.994 34760 Z= 0.323 Chirality : 0.042 0.202 3424 Planarity : 0.005 0.055 4222 Dihedral : 18.110 179.890 4791 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.79 % Allowed : 16.10 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.17), residues: 2256 helix: 2.50 (0.13), residues: 1436 sheet: None (None), residues: 0 loop : -0.72 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP W 50 HIS 0.007 0.001 HIS M 589 PHE 0.024 0.002 PHE X 8 TYR 0.018 0.002 TYR C 230 ARG 0.010 0.001 ARG 8 55 Details of bonding type rmsd hydrogen bonds : bond 0.04508 ( 1246) hydrogen bonds : angle 3.93517 ( 3663) covalent geometry : bond 0.00520 (24965) covalent geometry : angle 0.80287 (34760) Misc. bond : bond 0.07797 ( 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 366 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 311 time to evaluate : 2.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 9 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7729 (mp) REVERT: 0 27 ASP cc_start: 0.8541 (t70) cc_final: 0.8295 (t0) REVERT: 3 7 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.6950 (mp0) REVERT: 3 9 ARG cc_start: 0.7453 (ttp-170) cc_final: 0.6633 (ttt90) REVERT: 6 17 LEU cc_start: 0.8292 (mt) cc_final: 0.8073 (mt) REVERT: 7 9 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6795 (ttt180) REVERT: 8 20 ASN cc_start: 0.8432 (t0) cc_final: 0.8030 (m-40) REVERT: 9 17 LEU cc_start: 0.8438 (tp) cc_final: 0.7948 (mp) REVERT: B 31 LYS cc_start: 0.8893 (mttt) cc_final: 0.8637 (mmtp) REVERT: D 7 GLU cc_start: 0.7449 (tp30) cc_final: 0.6889 (mm-30) REVERT: D 9 ARG cc_start: 0.7422 (ttp-170) cc_final: 0.6807 (ttt-90) REVERT: G 31 LYS cc_start: 0.8635 (mttt) cc_final: 0.8373 (mttp) REVERT: I 7 ASN cc_start: 0.7474 (p0) cc_final: 0.7211 (p0) REVERT: I 31 LYS cc_start: 0.8885 (mtpt) cc_final: 0.8593 (mtmm) REVERT: L 151 ASP cc_start: 0.9155 (m-30) cc_final: 0.8817 (m-30) REVERT: L 181 TRP cc_start: 0.6991 (OUTLIER) cc_final: 0.5419 (t-100) REVERT: L 243 ASP cc_start: 0.7270 (t70) cc_final: 0.7031 (t0) REVERT: M 348 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7671 (mm-30) REVERT: P 38 TRP cc_start: 0.8960 (OUTLIER) cc_final: 0.8578 (t60) REVERT: Q 55 ARG cc_start: 0.7516 (ttm170) cc_final: 0.7262 (mtp180) REVERT: U 13 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8201 (tp40) REVERT: V 11 SER cc_start: 0.8838 (OUTLIER) cc_final: 0.8320 (p) REVERT: W 7 ASN cc_start: 0.6765 (p0) cc_final: 0.6506 (p0) REVERT: W 8 ASP cc_start: 0.7569 (p0) cc_final: 0.7073 (t0) REVERT: C 28 SER cc_start: 0.8224 (p) cc_final: 0.7967 (m) REVERT: C 106 MET cc_start: 0.7936 (ttm) cc_final: 0.7606 (ttm) REVERT: C 223 GLU cc_start: 0.8812 (tt0) cc_final: 0.8460 (tt0) REVERT: C 272 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.7626 (mp0) REVERT: Z 43 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8550 (tttp) outliers start: 55 outliers final: 25 residues processed: 349 average time/residue: 1.1965 time to fit residues: 489.9077 Evaluate side-chains 332 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 297 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 9 LEU Chi-restraints excluded: chain 3 residue 7 GLU Chi-restraints excluded: chain 3 residue 15 SER Chi-restraints excluded: chain 5 residue 13 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 B residue 12 ASP Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain L residue 8 LEU 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 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 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 P residue 38 TRP 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 V residue 11 SER 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 43 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 31 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 200 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 191 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 227 HIS O 13 GLN ** O 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 22 GLN U 7 ASN W 13 GLN ** 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 = 0.3234 r_free = 0.3234 target = 0.112771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.095232 restraints weight = 31384.790| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.19 r_work: 0.2814 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.480 25026 Z= 0.216 Angle : 0.820 16.254 34760 Z= 0.327 Chirality : 0.042 0.225 3424 Planarity : 0.005 0.053 4222 Dihedral : 18.088 179.869 4791 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.15 % Allowed : 16.10 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.17), residues: 2256 helix: 2.40 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.79 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP T 38 HIS 0.010 0.001 HIS L 227 PHE 0.026 0.002 PHE X 8 TYR 0.017 0.002 TYR M 424 ARG 0.011 0.001 ARG 8 55 Details of bonding type rmsd hydrogen bonds : bond 0.04548 ( 1246) hydrogen bonds : angle 3.99671 ( 3663) covalent geometry : bond 0.00541 (24965) covalent geometry : angle 0.82018 (34760) Misc. bond : bond 0.07702 ( 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 377 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 315 time to evaluate : 2.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 9 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7770 (mp) REVERT: 0 27 ASP cc_start: 0.8605 (t70) cc_final: 0.8304 (t0) REVERT: 0 38 ILE cc_start: 0.8583 (mm) cc_final: 0.8273 (mt) REVERT: 3 7 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.6998 (mp0) REVERT: 3 9 ARG cc_start: 0.7481 (ttp-170) cc_final: 0.6671 (ttt90) REVERT: 7 9 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.6871 (ttt180) REVERT: 8 20 ASN cc_start: 0.8430 (t0) cc_final: 0.8045 (m-40) REVERT: 9 17 LEU cc_start: 0.8343 (tp) cc_final: 0.7869 (mp) REVERT: B 31 LYS cc_start: 0.8900 (mttt) cc_final: 0.8639 (mmtp) REVERT: D 7 GLU cc_start: 0.7565 (tp30) cc_final: 0.6927 (mm-30) REVERT: D 9 ARG cc_start: 0.7417 (ttp-170) cc_final: 0.6793 (ttt-90) REVERT: G 31 LYS cc_start: 0.8666 (mttt) cc_final: 0.8447 (mttp) REVERT: I 7 ASN cc_start: 0.7651 (p0) cc_final: 0.7292 (p0) REVERT: I 31 LYS cc_start: 0.8907 (mtpt) cc_final: 0.8596 (mtmm) REVERT: L 151 ASP cc_start: 0.9193 (m-30) cc_final: 0.8888 (m-30) REVERT: L 181 TRP cc_start: 0.7107 (OUTLIER) cc_final: 0.5577 (t-100) REVERT: L 243 ASP cc_start: 0.7412 (t70) cc_final: 0.7179 (t0) REVERT: M 348 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7807 (mm-30) REVERT: M 505 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8730 (pt) REVERT: Q 55 ARG cc_start: 0.7546 (ttm170) cc_final: 0.7274 (mtp180) REVERT: U 13 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8212 (tp40) REVERT: V 11 SER cc_start: 0.8867 (OUTLIER) cc_final: 0.8384 (p) REVERT: W 7 ASN cc_start: 0.6845 (p0) cc_final: 0.6522 (p0) REVERT: W 8 ASP cc_start: 0.7588 (p0) cc_final: 0.7109 (t0) REVERT: C 28 SER cc_start: 0.8333 (p) cc_final: 0.8028 (m) REVERT: C 223 GLU cc_start: 0.8859 (tt0) cc_final: 0.8510 (tt0) REVERT: C 272 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.7683 (mp0) REVERT: Z 43 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8566 (tttp) REVERT: Z 56 LYS cc_start: 0.7942 (mmtm) cc_final: 0.7688 (mmtt) outliers start: 62 outliers final: 33 residues processed: 356 average time/residue: 1.2379 time to fit residues: 525.8054 Evaluate side-chains 339 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 296 time to evaluate : 2.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 9 LEU Chi-restraints excluded: chain 3 residue 7 GLU Chi-restraints excluded: chain 3 residue 15 SER Chi-restraints excluded: chain 5 residue 11 SER 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 B residue 12 ASP Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 110 VAL 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 290 LYS 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 505 ILE 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 11 SER 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 V residue 11 SER 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 Y residue 11 MET Chi-restraints excluded: chain Z residue 43 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 71 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 227 HIS O 13 GLN ** O 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 22 GLN U 7 ASN W 13 GLN Y 2 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.113603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.096164 restraints weight = 31192.811| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.22 r_work: 0.2814 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.478 25026 Z= 0.184 Angle : 0.781 15.917 34760 Z= 0.313 Chirality : 0.040 0.211 3424 Planarity : 0.005 0.053 4222 Dihedral : 17.883 179.906 4791 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.00 % Allowed : 16.66 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.17), residues: 2256 helix: 2.44 (0.13), residues: 1435 sheet: None (None), residues: 0 loop : -0.78 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 41 HIS 0.011 0.001 HIS L 227 PHE 0.026 0.002 PHE X 8 TYR 0.016 0.002 TYR C 133 ARG 0.011 0.000 ARG 8 55 Details of bonding type rmsd hydrogen bonds : bond 0.04404 ( 1246) hydrogen bonds : angle 3.94828 ( 3663) covalent geometry : bond 0.00458 (24965) covalent geometry : angle 0.78112 (34760) Misc. bond : bond 0.07548 ( 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 371 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 312 time to evaluate : 2.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 9 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7786 (mp) REVERT: 0 27 ASP cc_start: 0.8591 (t70) cc_final: 0.8237 (t0) REVERT: 0 38 ILE cc_start: 0.8623 (mm) cc_final: 0.8295 (mt) REVERT: 2 7 ASN cc_start: 0.7188 (p0) cc_final: 0.6404 (p0) REVERT: 3 7 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: 3 9 ARG cc_start: 0.7480 (ttp-170) cc_final: 0.6676 (ttt90) REVERT: 7 9 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6830 (ttt180) REVERT: 8 20 ASN cc_start: 0.8412 (t0) cc_final: 0.8028 (m-40) REVERT: 9 17 LEU cc_start: 0.8348 (tp) cc_final: 0.7959 (mm) REVERT: B 31 LYS cc_start: 0.8910 (mttt) cc_final: 0.8653 (mmtp) REVERT: D 9 ARG cc_start: 0.7298 (ttp-170) cc_final: 0.6778 (ttt-90) REVERT: E 20 ASN cc_start: 0.8605 (t0) cc_final: 0.8311 (m-40) REVERT: G 31 LYS cc_start: 0.8687 (mttt) cc_final: 0.8482 (mttp) REVERT: I 7 ASN cc_start: 0.7838 (p0) cc_final: 0.7314 (p0) REVERT: K 13 GLN cc_start: 0.7815 (tt0) cc_final: 0.7587 (tt0) REVERT: L 151 ASP cc_start: 0.9179 (m-30) cc_final: 0.8873 (m-30) REVERT: L 243 ASP cc_start: 0.7399 (t70) cc_final: 0.7175 (t0) REVERT: M 348 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7665 (mm-30) REVERT: M 505 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8726 (pt) REVERT: Q 55 ARG cc_start: 0.7560 (ttm170) cc_final: 0.7292 (mtp180) REVERT: U 13 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8206 (tp40) REVERT: V 11 SER cc_start: 0.8820 (OUTLIER) cc_final: 0.8397 (p) REVERT: W 7 ASN cc_start: 0.6893 (p0) cc_final: 0.6572 (p0) REVERT: W 8 ASP cc_start: 0.7522 (p0) cc_final: 0.7096 (t0) REVERT: C 28 SER cc_start: 0.8362 (p) cc_final: 0.8043 (m) REVERT: C 31 MET cc_start: 0.7190 (ttm) cc_final: 0.6791 (ttt) REVERT: C 223 GLU cc_start: 0.8865 (tt0) cc_final: 0.8527 (tt0) REVERT: C 236 MET cc_start: 0.7344 (OUTLIER) cc_final: 0.6224 (mtm) REVERT: C 272 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.7671 (mp0) REVERT: Z 43 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8565 (tttp) REVERT: Z 56 LYS cc_start: 0.7917 (mmtm) cc_final: 0.7677 (mmtt) outliers start: 59 outliers final: 30 residues processed: 349 average time/residue: 1.1572 time to fit residues: 474.1415 Evaluate side-chains 347 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 307 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 9 LEU Chi-restraints excluded: chain 3 residue 7 GLU 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 B residue 12 ASP Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain L residue 110 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 345 ASP 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 505 ILE 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 11 SER 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 V residue 11 SER Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Z residue 43 LYS 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 76 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 170 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 195 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 165 optimal weight: 0.5980 chunk 118 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 227 HIS O 13 GLN ** O 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 22 GLN U 7 ASN W 13 GLN Y 2 ASN 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 = 0.118585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.101479 restraints weight = 30494.798| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.06 r_work: 0.2895 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.411 25026 Z= 0.130 Angle : 0.697 14.473 34760 Z= 0.285 Chirality : 0.038 0.160 3424 Planarity : 0.004 0.052 4222 Dihedral : 17.401 179.988 4791 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.39 % Allowed : 17.42 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.17), residues: 2256 helix: 2.66 (0.13), residues: 1437 sheet: None (None), residues: 0 loop : -0.71 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 41 HIS 0.008 0.001 HIS L 227 PHE 0.027 0.001 PHE X 8 TYR 0.015 0.001 TYR C 133 ARG 0.013 0.000 ARG 8 55 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 1246) hydrogen bonds : angle 3.77254 ( 3663) covalent geometry : bond 0.00311 (24965) covalent geometry : angle 0.69676 (34760) Misc. bond : bond 0.06333 ( 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 377 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 330 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 9 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7780 (mp) REVERT: 0 27 ASP cc_start: 0.8505 (t70) cc_final: 0.8164 (t70) REVERT: 0 38 ILE cc_start: 0.8581 (mm) cc_final: 0.8284 (mt) REVERT: 2 7 ASN cc_start: 0.7160 (p0) cc_final: 0.6456 (p0) REVERT: 3 9 ARG cc_start: 0.7440 (ttp-170) cc_final: 0.6528 (ttt90) REVERT: 7 9 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.6726 (ttt180) REVERT: 9 17 LEU cc_start: 0.8295 (tp) cc_final: 0.7932 (mm) REVERT: B 31 LYS cc_start: 0.8853 (mttt) cc_final: 0.8458 (mmtt) REVERT: D 7 GLU cc_start: 0.7401 (tp30) cc_final: 0.6911 (mm-30) REVERT: D 9 ARG cc_start: 0.7258 (ttp-170) cc_final: 0.6733 (ttt-90) REVERT: G 31 LYS cc_start: 0.8648 (mttt) cc_final: 0.8416 (mttp) REVERT: I 7 ASN cc_start: 0.7861 (p0) cc_final: 0.7267 (p0) REVERT: I 31 LYS cc_start: 0.8865 (mtpt) cc_final: 0.8587 (mtmm) REVERT: J 9 ARG cc_start: 0.8140 (ttp-110) cc_final: 0.7293 (ptt90) REVERT: K 13 GLN cc_start: 0.7738 (tt0) cc_final: 0.7474 (tt0) REVERT: L 151 ASP cc_start: 0.9134 (m-30) cc_final: 0.8864 (m-30) REVERT: L 243 ASP cc_start: 0.7330 (t70) cc_final: 0.7121 (t0) REVERT: M 348 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7497 (mm-30) REVERT: M 505 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8616 (pt) REVERT: P 9 ARG cc_start: 0.8326 (ttp-170) cc_final: 0.8029 (ttp-110) REVERT: U 13 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8188 (tp40) REVERT: V 11 SER cc_start: 0.8639 (m) cc_final: 0.8296 (p) REVERT: W 7 ASN cc_start: 0.6918 (p0) cc_final: 0.6168 (p0) REVERT: W 8 ASP cc_start: 0.7436 (p0) cc_final: 0.7069 (t0) REVERT: C 106 MET cc_start: 0.7900 (ttm) cc_final: 0.7544 (ttm) REVERT: C 223 GLU cc_start: 0.8766 (tt0) cc_final: 0.8409 (tt0) REVERT: C 272 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7563 (mp0) REVERT: Z 43 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8369 (tttp) outliers start: 47 outliers final: 27 residues processed: 361 average time/residue: 1.1781 time to fit residues: 499.0742 Evaluate side-chains 344 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 310 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 9 LEU Chi-restraints excluded: chain 5 residue 11 SER 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 8 residue 32 THR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain L residue 110 VAL 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 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 27 ILE Chi-restraints excluded: chain C residue 75 LEU 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 Y residue 11 MET Chi-restraints excluded: chain Z residue 43 LYS Chi-restraints excluded: chain Z residue 47 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 192 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 121 optimal weight: 0.0370 chunk 39 optimal weight: 0.8980 chunk 166 optimal weight: 10.0000 chunk 189 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 129 optimal weight: 0.8980 overall best weight: 0.9660 ------------------------------------------------------------------------------- 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 Y 2 ASN 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 = 0.118229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.101002 restraints weight = 30517.148| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.12 r_work: 0.2887 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 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 : 0.004 0.401 25026 Z= 0.134 Angle : 0.702 14.138 34760 Z= 0.289 Chirality : 0.038 0.158 3424 Planarity : 0.004 0.054 4222 Dihedral : 17.159 179.970 4791 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.98 % Allowed : 18.38 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.17), residues: 2256 helix: 2.70 (0.12), residues: 1437 sheet: None (None), residues: 0 loop : -0.67 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 41 HIS 0.006 0.001 HIS M 589 PHE 0.026 0.001 PHE X 8 TYR 0.019 0.002 TYR Q 34 ARG 0.013 0.000 ARG 8 55 Details of bonding type rmsd hydrogen bonds : bond 0.04023 ( 1246) hydrogen bonds : angle 3.75249 ( 3663) covalent geometry : bond 0.00322 (24965) covalent geometry : angle 0.70173 (34760) Misc. bond : bond 0.06050 ( 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 356 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 317 time to evaluate : 2.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 9 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7830 (mp) REVERT: 0 27 ASP cc_start: 0.8531 (t70) cc_final: 0.8258 (t70) REVERT: 0 38 ILE cc_start: 0.8583 (mm) cc_final: 0.8288 (mt) REVERT: 2 7 ASN cc_start: 0.7158 (p0) cc_final: 0.6457 (p0) REVERT: 3 9 ARG cc_start: 0.7320 (ttp-170) cc_final: 0.6494 (ttt90) REVERT: 7 9 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6757 (ttt180) REVERT: 9 17 LEU cc_start: 0.8341 (tp) cc_final: 0.7929 (mm) REVERT: B 31 LYS cc_start: 0.8852 (mttt) cc_final: 0.8426 (mmtt) REVERT: D 9 ARG cc_start: 0.7205 (ttp-170) cc_final: 0.6705 (ttt-90) REVERT: G 31 LYS cc_start: 0.8640 (mttt) cc_final: 0.8431 (mttp) REVERT: J 9 ARG cc_start: 0.8145 (ttp-110) cc_final: 0.7309 (ptt90) REVERT: K 13 GLN cc_start: 0.7796 (tt0) cc_final: 0.7510 (tt0) REVERT: L 151 ASP cc_start: 0.9132 (m-30) cc_final: 0.8878 (m-30) REVERT: L 243 ASP cc_start: 0.7277 (t70) cc_final: 0.7061 (t0) REVERT: M 348 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7562 (mm-30) REVERT: M 505 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8619 (pt) REVERT: P 9 ARG cc_start: 0.8337 (ttp-170) cc_final: 0.8040 (ttp-110) REVERT: Q 34 TYR cc_start: 0.8496 (m-10) cc_final: 0.8291 (m-80) REVERT: S 38 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8699 (mp) REVERT: U 13 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8206 (tp40) REVERT: V 11 SER cc_start: 0.8627 (m) cc_final: 0.8272 (p) REVERT: C 28 SER cc_start: 0.8256 (p) cc_final: 0.7959 (m) REVERT: C 31 MET cc_start: 0.6947 (ttm) cc_final: 0.6372 (mmt) REVERT: C 106 MET cc_start: 0.7924 (ttm) cc_final: 0.7588 (ttm) REVERT: C 145 MET cc_start: 0.8647 (mmt) cc_final: 0.7538 (mmt) REVERT: C 223 GLU cc_start: 0.8812 (tt0) cc_final: 0.8433 (tt0) REVERT: Z 43 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8381 (ttpp) outliers start: 39 outliers final: 24 residues processed: 340 average time/residue: 1.1781 time to fit residues: 476.4253 Evaluate side-chains 337 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 306 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 9 LEU Chi-restraints excluded: chain 5 residue 11 SER 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 8 residue 32 THR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 285 SER Chi-restraints excluded: chain L residue 305 TRP Chi-restraints excluded: chain M residue 345 ASP 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 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 S residue 38 ILE Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain U residue 13 GLN Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain Y residue 11 MET Chi-restraints excluded: chain Z residue 43 LYS Chi-restraints excluded: chain Z residue 47 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 79 optimal weight: 0.0020 chunk 70 optimal weight: 0.9990 chunk 146 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 chunk 158 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 176 optimal weight: 5.9990 overall best weight: 3.1996 ------------------------------------------------------------------------------- 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 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 22 GLN 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 Y 2 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.112567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.095496 restraints weight = 30774.779| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.01 r_work: 0.2798 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.495 25026 Z= 0.239 Angle : 0.853 16.791 34760 Z= 0.343 Chirality : 0.043 0.232 3424 Planarity : 0.005 0.057 4222 Dihedral : 17.537 179.906 4791 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.08 % Allowed : 18.44 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.17), residues: 2256 helix: 2.37 (0.13), residues: 1436 sheet: None (None), residues: 0 loop : -0.76 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 41 HIS 0.009 0.002 HIS M 589 PHE 0.026 0.002 PHE X 8 TYR 0.020 0.002 TYR M 424 ARG 0.014 0.001 ARG 8 55 Details of bonding type rmsd hydrogen bonds : bond 0.04713 ( 1246) hydrogen bonds : angle 4.01412 ( 3663) covalent geometry : bond 0.00597 (24965) covalent geometry : angle 0.85337 (34760) Misc. bond : bond 0.07838 ( 61) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17427.33 seconds wall clock time: 307 minutes 8.96 seconds (18428.96 seconds total)