Starting phenix.real_space_refine on Fri Jun 20 02:25:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hjv_34839/06_2025/8hjv_34839.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hjv_34839/06_2025/8hjv_34839.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hjv_34839/06_2025/8hjv_34839.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hjv_34839/06_2025/8hjv_34839.map" model { file = "/net/cci-nas-00/data/ceres_data/8hjv_34839/06_2025/8hjv_34839.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hjv_34839/06_2025/8hjv_34839.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 5 7.16 5 P 3 5.49 5 Mg 48 5.21 5 S 71 5.16 5 C 15527 2.51 5 N 3231 2.21 5 O 3308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 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: 22193 Number of models: 1 Model: "" Number of chains: 68 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: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2337 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 16, 'TRANS': 277} 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: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 232 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} 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: "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: "C" Number of atoms: 2216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2216 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 23, 'TRANS': 267} 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: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "4" 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: "5" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "6" 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: "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: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "B" 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: "D" 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: "E" 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: "F" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "I" 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: "J" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 329 Unusual residues: {'BCL': 1, 'BPH': 3, 'MQE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "M" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 347 Unusual residues: {' FE': 1, 'BCL': 2, 'MQE': 2, 'PGV': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 69 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: 47 Chain: "N" 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: "O" 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: "P" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "Q" 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: "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: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "U" 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: "V" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 172 Unusual residues: {'HEM': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 14.02, per 1000 atoms: 0.63 Number of scatterers: 22193 At special positions: 0 Unit cell: (131.271, 138.415, 132.164, 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 71 16.00 P 3 15.00 Mg 48 11.99 O 3308 8.00 N 3231 7.00 C 15527 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=65, symmetry=0 Number of additional bonds: simple=65, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.39 Conformation dependent library (CDL) restraints added in 2.7 seconds 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4246 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 2 sheets defined 67.1% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain '0' and resid 20 through 51 removed outlier: 4.038A pdb=" N LEU 0 24 " --> pdb=" O ASN 0 20 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL 0 25 " --> pdb=" O ALA 0 21 " (cutoff:3.500A) Processing helix chain '1' and resid 8 through 34 removed outlier: 4.006A pdb=" N GLY 1 34 " --> pdb=" O VAL 1 30 " (cutoff:3.500A) Processing helix chain '2' and resid 19 through 51 removed outlier: 3.751A pdb=" N TRP 2 23 " --> pdb=" O ASN 2 19 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU 2 24 " --> pdb=" O ASN 2 20 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL 2 25 " --> pdb=" O ALA 2 21 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 34 removed outlier: 3.606A pdb=" N SER 3 11 " --> pdb=" O GLU 3 7 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY 3 34 " --> pdb=" O VAL 3 30 " (cutoff:3.500A) Processing helix chain '4' and resid 11 through 15 Processing helix chain '4' and resid 20 through 51 removed outlier: 4.037A pdb=" N LEU 4 24 " --> pdb=" O ASN 4 20 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL 4 25 " --> pdb=" O ALA 4 21 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 34 removed outlier: 3.605A pdb=" N SER 5 11 " --> pdb=" O GLU 5 7 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY 5 34 " --> pdb=" O VAL 5 30 " (cutoff:3.500A) Processing helix chain '6' and resid 20 through 51 removed outlier: 4.051A pdb=" N LEU 6 24 " --> pdb=" O ASN 6 20 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL 6 25 " --> pdb=" O ALA 6 21 " (cutoff:3.500A) Processing helix chain '7' and resid 7 through 34 removed outlier: 3.605A pdb=" N SER 7 11 " --> pdb=" O GLU 7 7 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY 7 34 " --> pdb=" O VAL 7 30 " (cutoff:3.500A) Processing helix chain '8' and resid 11 through 15 Processing helix chain '8' and resid 20 through 51 removed outlier: 4.281A pdb=" N LEU 8 24 " --> pdb=" O ASN 8 20 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL 8 25 " --> pdb=" O ALA 8 21 " (cutoff:3.500A) Processing helix chain '9' and resid 7 through 34 removed outlier: 3.605A pdb=" N SER 9 11 " --> pdb=" O GLU 9 7 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY 9 34 " --> pdb=" O VAL 9 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 34 removed outlier: 3.606A pdb=" N SER A 11 " --> pdb=" O GLU A 7 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 51 removed outlier: 4.038A pdb=" N LEU B 24 " --> pdb=" O ASN B 20 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR B 51 " --> pdb=" O CYS B 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 34 removed outlier: 3.606A pdb=" N SER D 11 " --> pdb=" O GLU D 7 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY D 34 " --> pdb=" O VAL D 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 51 removed outlier: 4.035A pdb=" N LEU E 24 " --> pdb=" O ASN E 20 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL E 25 " --> pdb=" O ALA E 21 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP E 48 " --> pdb=" O HIS E 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 34 removed outlier: 3.606A pdb=" N SER F 11 " --> pdb=" O GLU F 7 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY F 34 " --> pdb=" O VAL F 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 51 removed outlier: 4.122A pdb=" N LEU G 24 " --> pdb=" O ASN G 20 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL G 25 " --> pdb=" O ALA G 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 34 removed outlier: 3.606A pdb=" N SER H 11 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 4.006A 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 20 through 51 removed outlier: 4.054A pdb=" N LEU I 24 " --> pdb=" O ASN I 20 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL I 25 " --> pdb=" O ALA I 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 34 removed outlier: 3.607A pdb=" N SER J 11 " --> pdb=" O GLU J 7 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY J 34 " --> pdb=" O VAL J 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 51 removed outlier: 4.242A pdb=" N LEU K 24 " --> pdb=" O ASN K 20 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL K 25 " --> pdb=" O ALA K 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 43 removed outlier: 4.313A pdb=" N ILE L 39 " --> pdb=" O PRO L 35 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU L 40 " --> pdb=" O PHE L 36 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR L 43 " --> pdb=" O ILE L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 56 removed outlier: 3.772A pdb=" N PHE L 54 " --> pdb=" O LEU L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 93 removed outlier: 3.510A pdb=" N ILE L 75 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLY L 91 " --> pdb=" O TYR L 87 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL L 92 " --> pdb=" O LEU L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 113 Processing helix chain 'L' and resid 122 through 151 Processing helix chain 'L' and resid 154 through 172 removed outlier: 3.565A pdb=" N ILE L 158 " --> pdb=" O MET L 154 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL L 163 " --> pdb=" O ALA L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 179 Processing helix chain 'L' and resid 191 through 203 removed outlier: 3.685A pdb=" N TYR L 203 " --> pdb=" O ILE L 199 " (cutoff:3.500A) Processing helix chain 'L' and resid 205 through 208 Processing helix chain 'L' and resid 209 through 236 removed outlier: 3.647A pdb=" N GLU L 236 " --> pdb=" O ALA L 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 244 through 253 Processing helix chain 'L' and resid 259 through 288 removed outlier: 3.704A pdb=" N ILE L 263 " --> pdb=" O GLY L 259 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N HIS L 264 " --> pdb=" O GLU L 260 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG L 265 " --> pdb=" O ILE L 261 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL L 275 " --> pdb=" O GLY L 271 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU L 276 " --> pdb=" O ALA L 272 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR L 287 " --> pdb=" O PHE L 283 " (cutoff:3.500A) Processing helix chain 'L' and resid 294 through 306 removed outlier: 3.943A pdb=" N PHE L 298 " --> pdb=" O PHE L 295 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP L 300 " --> pdb=" O GLY L 297 " (cutoff:3.500A) Proline residue: L 303 - end of helix Processing helix chain 'M' and resid 338 through 342 Processing helix chain 'M' and resid 359 through 366 removed outlier: 3.698A pdb=" N GLY M 366 " --> pdb=" O GLN M 362 " (cutoff:3.500A) Processing helix chain 'M' and resid 376 through 402 removed outlier: 3.646A pdb=" N ILE M 381 " --> pdb=" O LEU M 377 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER M 382 " --> pdb=" O TRP M 378 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY M 398 " --> pdb=" O LEU M 394 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN M 400 " --> pdb=" O ASP M 396 " (cutoff:3.500A) Processing helix chain 'M' and resid 404 through 411 Processing helix chain 'M' and resid 412 through 415 removed outlier: 3.599A pdb=" N LEU M 415 " --> pdb=" O PHE M 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 412 through 415' Processing helix chain 'M' and resid 435 through 464 removed outlier: 4.067A pdb=" N LEU M 439 " --> pdb=" O GLY M 435 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA M 440 " --> pdb=" O GLY M 436 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY M 464 " --> pdb=" O ALA M 460 " (cutoff:3.500A) Processing helix chain 'M' and resid 467 through 485 removed outlier: 3.740A pdb=" N TRP M 471 " --> pdb=" O THR M 467 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU M 479 " --> pdb=" O SER M 475 " (cutoff:3.500A) Processing helix chain 'M' and resid 493 through 497 removed outlier: 3.740A pdb=" N ALA M 496 " --> pdb=" O ASN M 493 " (cutoff:3.500A) Processing helix chain 'M' and resid 501 through 517 removed outlier: 3.544A pdb=" N ILE M 505 " --> pdb=" O GLY M 501 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU M 506 " --> pdb=" O PHE M 502 " (cutoff:3.500A) Processing helix chain 'M' and resid 518 through 521 Processing helix chain 'M' and resid 522 through 549 Processing helix chain 'M' and resid 550 through 553 Processing helix chain 'M' and resid 556 through 563 removed outlier: 3.951A pdb=" N MET M 562 " --> pdb=" O PHE M 558 " (cutoff:3.500A) Processing helix chain 'M' and resid 565 through 580 removed outlier: 3.661A pdb=" N TRP M 575 " --> pdb=" O ALA M 571 " (cutoff:3.500A) Processing helix chain 'M' and resid 586 through 609 removed outlier: 3.850A pdb=" N ILE M 590 " --> pdb=" O TYR M 586 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA M 600 " --> pdb=" O ALA M 596 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU M 609 " --> pdb=" O ILE M 605 " (cutoff:3.500A) Processing helix chain 'M' and resid 616 through 624 removed outlier: 3.721A pdb=" N THR M 623 " --> pdb=" O ALA M 619 " (cutoff:3.500A) Processing helix chain 'M' and resid 634 through 638 removed outlier: 4.117A pdb=" N GLN M 637 " --> pdb=" O ASP M 634 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 34 removed outlier: 3.606A pdb=" N SER N 11 " --> pdb=" O GLU N 7 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY N 34 " --> pdb=" O VAL N 30 " (cutoff:3.500A) Processing helix chain 'O' and resid 20 through 51 removed outlier: 4.104A pdb=" N LEU O 24 " --> pdb=" O ASN O 20 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL O 25 " --> pdb=" O ALA O 21 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR O 51 " --> pdb=" O CYS O 47 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 34 removed outlier: 3.606A pdb=" N SER P 11 " --> pdb=" O GLU P 7 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY P 34 " --> pdb=" O VAL P 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 20 through 50 removed outlier: 4.050A pdb=" N LEU Q 24 " --> pdb=" O ASN Q 20 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL Q 25 " --> pdb=" O ALA Q 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 7 through 34 removed outlier: 3.607A pdb=" N SER R 11 " --> pdb=" O GLU R 7 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY R 34 " --> pdb=" O VAL R 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 20 through 50 removed outlier: 4.075A pdb=" N LEU S 24 " --> pdb=" O ASN S 20 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 34 removed outlier: 3.792A pdb=" N SER T 11 " --> pdb=" O GLU T 7 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY T 34 " --> pdb=" O VAL T 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 51 removed outlier: 3.752A pdb=" N TRP U 23 " --> pdb=" O ASN U 19 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU U 24 " --> pdb=" O ASN U 20 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL U 25 " --> pdb=" O ALA U 21 " (cutoff:3.500A) Processing helix chain 'V' and resid 8 through 32 removed outlier: 3.660A pdb=" N VAL V 12 " --> pdb=" O PHE V 8 " (cutoff:3.500A) Processing helix chain 'W' and resid 19 through 51 removed outlier: 3.752A pdb=" N TRP W 23 " --> pdb=" O ASN W 19 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU W 24 " --> pdb=" O ASN W 20 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL W 25 " --> pdb=" O ALA W 21 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 30 Proline residue: Y 19 - end of helix Processing helix chain 'C' and resid 31 through 47 Processing helix chain 'C' and resid 71 through 85 removed outlier: 3.697A pdb=" N ALA C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN C 85 " --> pdb=" O TYR C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 109 Processing helix chain 'C' and resid 109 through 115 Processing helix chain 'C' and resid 138 through 156 Processing helix chain 'C' and resid 218 through 236 Processing helix chain 'C' and resid 239 through 243 removed outlier: 4.030A pdb=" N CYS C 243 " --> pdb=" O CYS C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 274 removed outlier: 4.413A pdb=" N HIS C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER C 260 " --> pdb=" O GLN C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 298 removed outlier: 4.208A pdb=" N HIS C 297 " --> pdb=" O CYS C 293 " (cutoff:3.500A) Processing helix chain 'Z' and resid 18 through 47 removed outlier: 3.840A pdb=" N VAL Z 25 " --> pdb=" O ALA Z 21 " (cutoff:3.500A) Proline residue: Z 26 - end of helix removed outlier: 4.093A pdb=" N ILE Z 31 " --> pdb=" O LEU Z 27 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG Z 39 " --> pdb=" O ILE Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 53 through 58 removed outlier: 3.735A pdb=" N ASN Z 58 " --> pdb=" O PRO Z 54 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 7 through 9 Processing sheet with id=AA2, first strand: chain 'L' and resid 32 through 34 removed outlier: 4.073A pdb=" N TYR Z 49 " --> pdb=" O ILE L 34 " (cutoff:3.500A) 1114 hydrogen bonds defined for protein. 3276 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.90 Time building geometry restraints manager: 9.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.30: 2963 1.30 - 1.49: 10509 1.49 - 1.69: 9434 1.69 - 1.88: 119 1.88 - 2.08: 208 Bond restraints: 23233 Sorted by residual: bond pdb=" C HIS W 26 " pdb=" N ASP W 27 " ideal model delta sigma weight residual 1.334 1.221 0.113 1.27e-02 6.20e+03 7.91e+01 bond pdb=" C HIS U 44 " pdb=" N VAL U 45 " ideal model delta sigma weight residual 1.334 1.441 -0.107 1.26e-02 6.30e+03 7.20e+01 bond pdb=" C VAL 0 25 " pdb=" N HIS 0 26 " ideal model delta sigma weight residual 1.335 1.449 -0.115 1.36e-02 5.41e+03 7.10e+01 bond pdb=" C ILE 3 26 " pdb=" N HIS 3 27 " ideal model delta sigma weight residual 1.334 1.228 0.106 1.27e-02 6.20e+03 7.01e+01 bond pdb=" C HIS 1 27 " pdb=" N PHE 1 28 " ideal model delta sigma weight residual 1.334 1.442 -0.107 1.33e-02 5.65e+03 6.50e+01 ... (remaining 23228 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.78: 29974 3.78 - 7.57: 2117 7.57 - 11.35: 344 11.35 - 15.14: 74 15.14 - 18.92: 3 Bond angle restraints: 32512 Sorted by residual: angle pdb=" N TRP Q 48 " pdb=" CA TRP Q 48 " pdb=" C TRP Q 48 " ideal model delta sigma weight residual 112.12 100.96 11.16 1.34e+00 5.57e-01 6.94e+01 angle pdb=" N ALA C 51 " pdb=" CA ALA C 51 " pdb=" C ALA C 51 " ideal model delta sigma weight residual 109.72 119.92 -10.20 1.25e+00 6.40e-01 6.66e+01 angle pdb=" N TRP S 48 " pdb=" CA TRP S 48 " pdb=" C TRP S 48 " ideal model delta sigma weight residual 112.93 103.45 9.48 1.33e+00 5.65e-01 5.08e+01 angle pdb=" N TRP B 48 " pdb=" CA TRP B 48 " pdb=" C TRP B 48 " ideal model delta sigma weight residual 113.12 104.50 8.62 1.25e+00 6.40e-01 4.76e+01 angle pdb=" N ASP W 8 " pdb=" CA ASP W 8 " pdb=" C ASP W 8 " ideal model delta sigma weight residual 110.68 120.17 -9.49 1.39e+00 5.18e-01 4.66e+01 ... (remaining 32507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.05: 11353 35.05 - 70.10: 724 70.10 - 105.15: 54 105.15 - 140.19: 7 140.19 - 175.24: 3 Dihedral angle restraints: 12141 sinusoidal: 5608 harmonic: 6533 Sorted by residual: dihedral pdb=" C1 BCL V 101 " pdb=" CGA BCL V 101 " pdb=" O2A BCL V 101 " pdb=" CBA BCL V 101 " ideal model delta sinusoidal sigma weight residual 180.00 51.14 128.86 1 6.00e+00 2.78e-02 4.34e+02 dihedral pdb=" C1 BCL L 401 " pdb=" CGA BCL L 401 " pdb=" O2A BCL L 401 " pdb=" CBA BCL L 401 " ideal model delta sinusoidal sigma weight residual -180.00 -65.07 -114.93 1 6.00e+00 2.78e-02 3.79e+02 dihedral pdb=" CBD BCL W 101 " pdb=" CGD BCL W 101 " pdb=" O2D BCL W 101 " pdb=" CED BCL W 101 " ideal model delta sinusoidal sigma weight residual -180.00 -94.58 -85.42 1 5.00e+00 4.00e-02 3.53e+02 ... (remaining 12138 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.125: 3301 1.125 - 2.250: 0 2.250 - 3.374: 0 3.374 - 4.499: 0 4.499 - 5.624: 27 Chirality restraints: 3328 Sorted by residual: chirality pdb=" C18 BCL Q 101 " pdb=" C17 BCL Q 101 " pdb=" C19 BCL Q 101 " pdb=" C20 BCL Q 101 " both_signs ideal model delta sigma weight residual False 2.71 -2.91 5.62 2.00e-01 2.50e+01 7.91e+02 chirality pdb=" C18 BCL E 101 " pdb=" C17 BCL E 101 " pdb=" C19 BCL E 101 " pdb=" C20 BCL E 101 " both_signs ideal model delta sigma weight residual False 2.71 -2.91 5.62 2.00e-01 2.50e+01 7.90e+02 chirality pdb=" C18 BCL I 101 " pdb=" C17 BCL I 101 " pdb=" C19 BCL I 101 " pdb=" C20 BCL I 101 " both_signs ideal model delta sigma weight residual False 2.71 -2.91 5.62 2.00e-01 2.50e+01 7.89e+02 ... (remaining 3325 not shown) Planarity restraints: 3826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL 2 101 " -0.355 1.50e-02 4.44e+03 3.03e-01 2.04e+03 pdb=" C2 BCL 2 101 " 0.475 1.50e-02 4.44e+03 pdb=" C3 BCL 2 101 " 0.193 1.50e-02 4.44e+03 pdb=" C4 BCL 2 101 " -0.258 1.50e-02 4.44e+03 pdb=" C5 BCL 2 101 " -0.055 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL L 401 " 0.353 1.50e-02 4.44e+03 2.99e-01 1.98e+03 pdb=" C2 BCL L 401 " -0.446 1.50e-02 4.44e+03 pdb=" C3 BCL L 401 " -0.220 1.50e-02 4.44e+03 pdb=" C4 BCL L 401 " 0.043 1.50e-02 4.44e+03 pdb=" C5 BCL L 401 " 0.270 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C3D BCL V 101 " -0.051 5.00e-03 4.00e+04 9.42e-02 1.42e+03 pdb=" CAD BCL V 101 " 0.162 5.00e-03 4.00e+04 pdb=" CBD BCL V 101 " -0.044 5.00e-03 4.00e+04 pdb=" OBD BCL V 101 " -0.067 5.00e-03 4.00e+04 ... (remaining 3823 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 119 2.50 - 3.10: 15855 3.10 - 3.70: 32319 3.70 - 4.30: 47300 4.30 - 4.90: 77676 Nonbonded interactions: 173269 Sorted by model distance: nonbonded pdb=" NH1 ARG Z 39 " pdb=" CG LYS Z 43 " model vdw 1.901 3.520 nonbonded pdb=" OE2 GLU M 557 " pdb="FE FE M1004 " model vdw 1.961 2.260 nonbonded pdb=" OE1 GLU M 557 " pdb="FE FE M1004 " model vdw 2.016 2.260 nonbonded pdb=" ND2 ASN M 518 " pdb=" CE2 TYR M 521 " model vdw 2.053 3.420 nonbonded pdb=" NH2 ARG M 570 " pdb=" ND2 ASN Z 58 " model vdw 2.072 3.200 ... (remaining 173264 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' selection = chain '2' selection = chain '4' selection = chain '6' selection = chain '8' selection = chain 'B' selection = chain 'E' selection = chain 'G' selection = (chain 'I' and (resid 7 through 55 or resid 101 through 102)) selection = chain 'K' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } 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) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.970 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 50.190 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 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 : 0.023 0.711 23298 Z= 1.470 Angle : 2.022 18.919 32512 Z= 0.872 Chirality : 0.517 5.624 3328 Planarity : 0.039 0.303 3826 Dihedral : 20.900 175.242 7895 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.99 % Allowed : 13.11 % Favored : 85.90 % Cbeta Deviations : 0.09 % 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: -0.85 (0.16), residues: 2193 helix: 0.51 (0.13), residues: 1327 sheet: None (None), residues: 0 loop : -2.33 (0.18), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 2 53 HIS 0.008 0.001 HIS L 192 PHE 0.022 0.002 PHE H 6 TYR 0.014 0.002 TYR M 408 ARG 0.004 0.000 ARG D 4 Details of bonding type rmsd hydrogen bonds : bond 0.15682 ( 1114) hydrogen bonds : angle 5.49188 ( 3276) covalent geometry : bond 0.01926 (23233) covalent geometry : angle 2.02177 (32512) Misc. bond : bond 0.22750 ( 65) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 575 time to evaluate : 2.282 Fit side-chains revert: symmetry clash REVERT: 0 15 LYS cc_start: 0.7862 (tppt) cc_final: 0.7295 (tptp) REVERT: 1 24 LEU cc_start: 0.8218 (mt) cc_final: 0.8000 (mp) REVERT: 2 52 PRO cc_start: 0.6655 (Cg_endo) cc_final: 0.6433 (Cg_exo) REVERT: 4 9 LEU cc_start: 0.7346 (mt) cc_final: 0.6973 (tp) REVERT: 5 27 HIS cc_start: 0.8183 (OUTLIER) cc_final: 0.7946 (m90) REVERT: 6 28 ILE cc_start: 0.8113 (mt) cc_final: 0.7881 (mm) REVERT: A 27 HIS cc_start: 0.8413 (OUTLIER) cc_final: 0.7977 (m90) REVERT: A 40 ARG cc_start: 0.5896 (ttm-80) cc_final: 0.5677 (ttt90) REVERT: B 34 TYR cc_start: 0.7889 (m-10) cc_final: 0.7612 (m-10) REVERT: E 31 LYS cc_start: 0.7821 (mttt) cc_final: 0.7451 (mmmt) REVERT: E 46 LEU cc_start: 0.8081 (mt) cc_final: 0.7825 (mt) REVERT: H 7 GLU cc_start: 0.6269 (mt-10) cc_final: 0.5319 (mp0) REVERT: I 31 LYS cc_start: 0.7125 (mttt) cc_final: 0.6775 (mtpt) REVERT: J 6 PHE cc_start: 0.6033 (m-80) cc_final: 0.5729 (m-80) REVERT: K 8 ASP cc_start: 0.7899 (p0) cc_final: 0.7524 (p0) REVERT: K 13 GLN cc_start: 0.6634 (tt0) cc_final: 0.6399 (mp10) REVERT: K 24 LEU cc_start: 0.7343 (mt) cc_final: 0.6939 (mt) REVERT: K 51 THR cc_start: 0.7993 (p) cc_final: 0.7784 (m) REVERT: L 16 LEU cc_start: 0.5427 (tp) cc_final: 0.5224 (tp) REVERT: L 58 ASP cc_start: 0.6848 (t70) cc_final: 0.6049 (t70) REVERT: L 302 MET cc_start: 0.7224 (mmm) cc_final: 0.6992 (mmm) REVERT: M 503 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7384 (ttp-170) REVERT: M 632 ASN cc_start: 0.7674 (p0) cc_final: 0.7458 (p0) REVERT: P 27 HIS cc_start: 0.8449 (OUTLIER) cc_final: 0.7886 (m90) REVERT: R 27 HIS cc_start: 0.8328 (OUTLIER) cc_final: 0.7656 (m90) REVERT: S 15 LYS cc_start: 0.7134 (ttmm) cc_final: 0.6803 (tptt) REVERT: W 31 LYS cc_start: 0.6744 (mttt) cc_final: 0.6317 (mmmt) REVERT: W 41 VAL cc_start: 0.7041 (t) cc_final: 0.6828 (m) REVERT: C 148 MET cc_start: 0.8797 (ttp) cc_final: 0.8553 (ttp) outliers start: 19 outliers final: 6 residues processed: 591 average time/residue: 0.3422 time to fit residues: 315.0748 Evaluate side-chains 340 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 329 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 27 HIS Chi-restraints excluded: chain 5 residue 27 HIS Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain D residue 27 HIS Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain M residue 503 ARG Chi-restraints excluded: chain P residue 27 HIS Chi-restraints excluded: chain R residue 27 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 0.4980 chunk 151 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 chunk 156 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 181 optimal weight: 10.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 GLN B 13 GLN E 7 ASN G 7 ASN H 37 ASN K 19 ASN L 306 ASN T 37 ASN U 19 ASN W 20 ASN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN C 155 ASN C 233 ASN ** 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 = 0.3652 r_free = 0.3652 target = 0.124423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.104749 restraints weight = 40888.249| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.31 r_work: 0.3217 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.428 23298 Z= 0.179 Angle : 1.005 17.110 32512 Z= 0.364 Chirality : 0.043 0.194 3328 Planarity : 0.005 0.046 3826 Dihedral : 21.546 179.332 4025 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.60 % Allowed : 15.72 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.41 (0.18), residues: 2193 helix: 2.49 (0.13), residues: 1349 sheet: None (None), residues: 0 loop : -1.83 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 38 HIS 0.006 0.001 HIS L 192 PHE 0.015 0.001 PHE L 62 TYR 0.017 0.001 TYR M 521 ARG 0.006 0.000 ARG 1 40 Details of bonding type rmsd hydrogen bonds : bond 0.06434 ( 1114) hydrogen bonds : angle 3.70175 ( 3276) covalent geometry : bond 0.00458 (23233) covalent geometry : angle 1.00453 (32512) Misc. bond : bond 0.07865 ( 65) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 357 time to evaluate : 3.085 Fit side-chains revert: symmetry clash REVERT: 0 15 LYS cc_start: 0.8099 (tppt) cc_final: 0.7323 (tptp) REVERT: 2 52 PRO cc_start: 0.6320 (Cg_endo) cc_final: 0.5918 (Cg_exo) REVERT: 4 9 LEU cc_start: 0.7607 (mt) cc_final: 0.7177 (tp) REVERT: 6 28 ILE cc_start: 0.8115 (mt) cc_final: 0.7886 (mm) REVERT: B 34 TYR cc_start: 0.8039 (m-10) cc_final: 0.7784 (m-10) REVERT: E 31 LYS cc_start: 0.7879 (mttt) cc_final: 0.7547 (mmmt) REVERT: G 8 ASP cc_start: 0.6258 (p0) cc_final: 0.6012 (p0) REVERT: H 7 GLU cc_start: 0.6458 (mt-10) cc_final: 0.5383 (mp0) REVERT: I 22 GLN cc_start: 0.8208 (mt0) cc_final: 0.7841 (mt0) REVERT: K 13 GLN cc_start: 0.6954 (tt0) cc_final: 0.6397 (mp10) REVERT: K 24 LEU cc_start: 0.7406 (mt) cc_final: 0.6859 (mt) REVERT: L 16 LEU cc_start: 0.5448 (tp) cc_final: 0.5188 (tp) REVERT: L 39 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7688 (pt) REVERT: L 58 ASP cc_start: 0.6490 (t70) cc_final: 0.6212 (t70) REVERT: M 357 HIS cc_start: 0.7389 (OUTLIER) cc_final: 0.6718 (t70) REVERT: M 387 PHE cc_start: 0.7610 (t80) cc_final: 0.7182 (t80) REVERT: M 396 ASP cc_start: 0.8484 (t0) cc_final: 0.8228 (t0) REVERT: M 632 ASN cc_start: 0.7706 (p0) cc_final: 0.7500 (p0) REVERT: O 55 ARG cc_start: 0.6873 (OUTLIER) cc_final: 0.6671 (ptp-110) REVERT: P 24 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7858 (mp) REVERT: P 27 HIS cc_start: 0.9095 (OUTLIER) cc_final: 0.8752 (m90) REVERT: Q 34 TYR cc_start: 0.7108 (m-10) cc_final: 0.6739 (m-10) REVERT: R 27 HIS cc_start: 0.9063 (OUTLIER) cc_final: 0.8283 (m90) REVERT: S 15 LYS cc_start: 0.7475 (ttmm) cc_final: 0.6938 (tptt) REVERT: U 41 VAL cc_start: 0.8480 (t) cc_final: 0.8217 (p) REVERT: V 22 MET cc_start: 0.6543 (mmp) cc_final: 0.6157 (mmp) REVERT: W 31 LYS cc_start: 0.6602 (mttt) cc_final: 0.6156 (mmmt) REVERT: W 55 ARG cc_start: 0.6343 (ttp-170) cc_final: 0.6095 (ttm170) REVERT: Y 17 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.7781 (t80) REVERT: C 31 MET cc_start: 0.5564 (mtp) cc_final: 0.5248 (mtt) REVERT: C 122 HIS cc_start: 0.7605 (OUTLIER) cc_final: 0.7086 (m-70) REVERT: C 145 MET cc_start: 0.8288 (mmt) cc_final: 0.7854 (mmt) REVERT: C 148 MET cc_start: 0.8922 (ttp) cc_final: 0.8648 (ttp) REVERT: C 229 MET cc_start: 0.8663 (mmt) cc_final: 0.8343 (mmt) REVERT: C 244 HIS cc_start: 0.8692 (OUTLIER) cc_final: 0.8079 (t-90) outliers start: 69 outliers final: 39 residues processed: 402 average time/residue: 0.3146 time to fit residues: 204.9834 Evaluate side-chains 352 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 304 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 3 residue 27 HIS Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 7 residue 14 VAL Chi-restraints excluded: chain 7 residue 33 SER Chi-restraints excluded: chain 9 residue 15 SER Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 145 ASP Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 304 ILE Chi-restraints excluded: chain M residue 357 HIS Chi-restraints excluded: chain M residue 367 GLU Chi-restraints excluded: chain M residue 429 ASN Chi-restraints excluded: chain M residue 449 VAL Chi-restraints excluded: chain M residue 493 ASN Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain N residue 27 HIS Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 47 CYS Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 27 HIS Chi-restraints excluded: chain Q residue 12 ASP Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain R residue 27 HIS Chi-restraints excluded: chain T residue 11 SER Chi-restraints excluded: chain W residue 10 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain Y residue 17 PHE Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 312 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 64 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 157 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 71 optimal weight: 0.0060 chunk 74 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 chunk 199 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 144 optimal weight: 5.9990 overall best weight: 4.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 26 HIS B 13 GLN L 183 HIS L 205 ASN L 252 ASN M 525 HIS P 37 ASN S 22 GLN W 19 ASN C 87 GLN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN C 168 GLN C 269 HIS Z 58 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.115947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.095388 restraints weight = 40953.989| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.57 r_work: 0.3046 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.414 23298 Z= 0.296 Angle : 1.077 20.892 32512 Z= 0.398 Chirality : 0.047 0.301 3328 Planarity : 0.005 0.048 3826 Dihedral : 20.438 179.769 4015 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.23 % Allowed : 14.62 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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: 1.53 (0.18), residues: 2193 helix: 2.67 (0.13), residues: 1353 sheet: None (None), residues: 0 loop : -1.97 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 38 HIS 0.009 0.002 HIS L 192 PHE 0.029 0.002 PHE M 519 TYR 0.023 0.002 TYR M 424 ARG 0.006 0.001 ARG P 4 Details of bonding type rmsd hydrogen bonds : bond 0.06903 ( 1114) hydrogen bonds : angle 3.64719 ( 3276) covalent geometry : bond 0.00595 (23233) covalent geometry : angle 1.07742 (32512) Misc. bond : bond 0.07592 ( 65) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 318 time to evaluate : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 15 LYS cc_start: 0.8217 (tppt) cc_final: 0.7411 (tptp) REVERT: 2 7 ASN cc_start: 0.4355 (p0) cc_final: 0.4125 (p0) REVERT: 2 31 LYS cc_start: 0.6669 (mttt) cc_final: 0.6440 (mttt) REVERT: 4 9 LEU cc_start: 0.7710 (mt) cc_final: 0.7197 (tp) REVERT: 6 15 LYS cc_start: 0.8052 (mttt) cc_final: 0.7753 (mmtt) REVERT: 6 28 ILE cc_start: 0.8351 (mt) cc_final: 0.8110 (mm) REVERT: 8 22 GLN cc_start: 0.7897 (mp10) cc_final: 0.7675 (mp10) REVERT: 8 41 VAL cc_start: 0.8587 (t) cc_final: 0.8161 (p) REVERT: E 31 LYS cc_start: 0.7990 (mttt) cc_final: 0.7631 (mmmt) REVERT: H 7 GLU cc_start: 0.6485 (mt-10) cc_final: 0.5612 (mp0) REVERT: J 7 GLU cc_start: 0.6650 (mt-10) cc_final: 0.6431 (mt-10) REVERT: K 13 GLN cc_start: 0.6822 (tt0) cc_final: 0.6450 (mp10) REVERT: L 16 LEU cc_start: 0.5708 (tp) cc_final: 0.5354 (tp) REVERT: L 53 ARG cc_start: 0.7193 (mtm-85) cc_final: 0.6933 (mtm-85) REVERT: L 64 ILE cc_start: 0.8361 (tt) cc_final: 0.7997 (tp) REVERT: L 302 MET cc_start: 0.8012 (mmm) cc_final: 0.7486 (mtp) REVERT: M 387 PHE cc_start: 0.7647 (t80) cc_final: 0.7227 (t80) REVERT: M 429 ASN cc_start: 0.8787 (OUTLIER) cc_final: 0.8571 (m-40) REVERT: M 551 LYS cc_start: 0.6208 (OUTLIER) cc_final: 0.5531 (tmtt) REVERT: M 630 TRP cc_start: 0.8509 (OUTLIER) cc_final: 0.8016 (t60) REVERT: O 20 ASN cc_start: 0.7784 (t0) cc_final: 0.7521 (m-40) REVERT: O 42 ILE cc_start: 0.9166 (mt) cc_final: 0.8925 (mm) REVERT: Q 55 ARG cc_start: 0.6964 (ttm110) cc_final: 0.6329 (ttp-170) REVERT: R 27 HIS cc_start: 0.9297 (OUTLIER) cc_final: 0.8207 (m90) REVERT: S 15 LYS cc_start: 0.7308 (ttmm) cc_final: 0.7004 (tptt) REVERT: S 37 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8010 (mm) REVERT: V 22 MET cc_start: 0.7138 (mmp) cc_final: 0.6760 (mmp) REVERT: W 30 VAL cc_start: 0.6767 (t) cc_final: 0.6351 (m) REVERT: W 31 LYS cc_start: 0.6570 (mttt) cc_final: 0.6106 (mmmt) REVERT: W 41 VAL cc_start: 0.6854 (t) cc_final: 0.6577 (m) REVERT: W 55 ARG cc_start: 0.6521 (ttp-170) cc_final: 0.6195 (ttm170) REVERT: Y 17 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.7740 (t80) REVERT: C 122 HIS cc_start: 0.7617 (OUTLIER) cc_final: 0.6955 (m-70) REVERT: C 145 MET cc_start: 0.8398 (mmt) cc_final: 0.8051 (mmt) outliers start: 81 outliers final: 54 residues processed: 375 average time/residue: 0.3119 time to fit residues: 186.5670 Evaluate side-chains 339 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 278 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 3 residue 14 VAL Chi-restraints excluded: chain 3 residue 38 TRP Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 6 residue 54 ILE Chi-restraints excluded: chain 7 residue 14 VAL Chi-restraints excluded: chain 7 residue 33 SER Chi-restraints excluded: chain 9 residue 15 SER Chi-restraints excluded: chain 9 residue 18 LEU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain K residue 7 ASN Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 145 ASP Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 367 GLU Chi-restraints excluded: chain M residue 429 ASN Chi-restraints excluded: chain M residue 449 VAL Chi-restraints excluded: chain M residue 493 ASN Chi-restraints excluded: chain M residue 551 LYS Chi-restraints excluded: chain M residue 613 LEU Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 12 ASP Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 47 CYS Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 27 HIS Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain U residue 30 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 39 ILE Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain Y residue 17 PHE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 293 CYS Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain Z residue 25 VAL Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain Z residue 58 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 153 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 147 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.115473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.095453 restraints weight = 41225.129| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.26 r_work: 0.3070 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.302 23298 Z= 0.176 Angle : 0.946 17.113 32512 Z= 0.345 Chirality : 0.042 0.234 3328 Planarity : 0.005 0.094 3826 Dihedral : 19.447 179.687 4009 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.71 % Allowed : 16.19 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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: 1.80 (0.18), residues: 2193 helix: 2.92 (0.13), residues: 1354 sheet: None (None), residues: 0 loop : -1.94 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 38 HIS 0.006 0.001 HIS L 192 PHE 0.019 0.001 PHE M 519 TYR 0.019 0.002 TYR M 424 ARG 0.003 0.001 ARG 4 55 Details of bonding type rmsd hydrogen bonds : bond 0.06155 ( 1114) hydrogen bonds : angle 3.48063 ( 3276) covalent geometry : bond 0.00439 (23233) covalent geometry : angle 0.94551 (32512) Misc. bond : bond 0.06189 ( 65) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 302 time to evaluate : 2.421 Fit side-chains revert: symmetry clash REVERT: 0 15 LYS cc_start: 0.8089 (tppt) cc_final: 0.7371 (tptp) REVERT: 2 7 ASN cc_start: 0.4293 (p0) cc_final: 0.3986 (p0) REVERT: 2 31 LYS cc_start: 0.6607 (mttt) cc_final: 0.6372 (mttt) REVERT: 4 9 LEU cc_start: 0.7639 (mt) cc_final: 0.7252 (tp) REVERT: 6 15 LYS cc_start: 0.7989 (mttt) cc_final: 0.7717 (mmtt) REVERT: 6 28 ILE cc_start: 0.8284 (mt) cc_final: 0.8045 (mm) REVERT: 8 41 VAL cc_start: 0.8537 (t) cc_final: 0.8119 (p) REVERT: E 31 LYS cc_start: 0.7992 (mttt) cc_final: 0.7682 (mmmt) REVERT: H 7 GLU cc_start: 0.6445 (mt-10) cc_final: 0.5620 (mp0) REVERT: J 7 GLU cc_start: 0.6676 (mt-10) cc_final: 0.6401 (mt-10) REVERT: L 16 LEU cc_start: 0.5709 (tp) cc_final: 0.5387 (tp) REVERT: L 64 ILE cc_start: 0.8514 (tt) cc_final: 0.8137 (tp) REVERT: L 253 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7450 (mm) REVERT: L 302 MET cc_start: 0.7937 (mmm) cc_final: 0.7368 (mtp) REVERT: M 387 PHE cc_start: 0.7575 (t80) cc_final: 0.7194 (t80) REVERT: O 42 ILE cc_start: 0.9154 (mt) cc_final: 0.8945 (mm) REVERT: Q 55 ARG cc_start: 0.6963 (ttm110) cc_final: 0.6322 (ttp-170) REVERT: S 15 LYS cc_start: 0.7214 (ttmm) cc_final: 0.6941 (tptt) REVERT: U 22 GLN cc_start: 0.6964 (OUTLIER) cc_final: 0.6574 (mp10) REVERT: W 13 GLN cc_start: 0.6151 (tm-30) cc_final: 0.5753 (tm-30) REVERT: W 30 VAL cc_start: 0.6725 (t) cc_final: 0.6351 (m) REVERT: W 38 ILE cc_start: 0.7120 (OUTLIER) cc_final: 0.6883 (mp) REVERT: W 41 VAL cc_start: 0.6881 (t) cc_final: 0.6611 (m) REVERT: W 55 ARG cc_start: 0.6611 (ttp-170) cc_final: 0.6228 (ttm170) REVERT: Y 17 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.7730 (t80) REVERT: C 87 GLN cc_start: 0.7529 (mp10) cc_final: 0.6996 (mp-120) REVERT: C 122 HIS cc_start: 0.7355 (OUTLIER) cc_final: 0.6656 (m-70) REVERT: C 145 MET cc_start: 0.8352 (mmt) cc_final: 0.8041 (mmt) REVERT: C 229 MET cc_start: 0.8916 (mmt) cc_final: 0.8479 (mmt) outliers start: 71 outliers final: 50 residues processed: 358 average time/residue: 0.3906 time to fit residues: 228.8816 Evaluate side-chains 334 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 279 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 3 residue 38 TRP Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 5 residue 24 LEU Chi-restraints excluded: chain 7 residue 14 VAL Chi-restraints excluded: chain 7 residue 33 SER Chi-restraints excluded: chain 9 residue 18 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain K residue 7 ASN Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 304 ILE Chi-restraints excluded: chain L residue 308 VAL Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 449 VAL Chi-restraints excluded: chain M residue 493 ASN Chi-restraints excluded: chain M residue 613 LEU Chi-restraints excluded: chain O residue 12 ASP Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 47 CYS Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain U residue 22 GLN Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 38 ILE Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain Y residue 17 PHE Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 293 CYS Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain Z residue 25 VAL Chi-restraints excluded: chain Z residue 53 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 194 optimal weight: 5.9990 chunk 78 optimal weight: 0.0970 chunk 190 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 169 optimal weight: 0.1980 chunk 162 optimal weight: 9.9990 chunk 145 optimal weight: 8.9990 chunk 195 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN C 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.119493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.099033 restraints weight = 40176.308| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.41 r_work: 0.3144 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.267 23298 Z= 0.124 Angle : 0.835 16.293 32512 Z= 0.302 Chirality : 0.039 0.201 3328 Planarity : 0.004 0.100 3826 Dihedral : 18.413 179.754 4007 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.66 % Allowed : 17.08 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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: 2.11 (0.18), residues: 2193 helix: 3.20 (0.13), residues: 1370 sheet: None (None), residues: 0 loop : -2.00 (0.20), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 38 HIS 0.005 0.001 HIS M 525 PHE 0.014 0.001 PHE L 62 TYR 0.017 0.001 TYR O 34 ARG 0.004 0.000 ARG P 40 Details of bonding type rmsd hydrogen bonds : bond 0.04827 ( 1114) hydrogen bonds : angle 3.24530 ( 3276) covalent geometry : bond 0.00301 (23233) covalent geometry : angle 0.83461 (32512) Misc. bond : bond 0.04867 ( 65) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 306 time to evaluate : 3.184 Fit side-chains REVERT: 0 15 LYS cc_start: 0.8028 (tppt) cc_final: 0.7303 (tptp) REVERT: 2 7 ASN cc_start: 0.3976 (p0) cc_final: 0.3760 (p0) REVERT: 4 9 LEU cc_start: 0.7684 (mt) cc_final: 0.7326 (tp) REVERT: 6 15 LYS cc_start: 0.7983 (mttt) cc_final: 0.7673 (mmtt) REVERT: 6 28 ILE cc_start: 0.8217 (mt) cc_final: 0.7962 (mm) REVERT: 8 41 VAL cc_start: 0.8351 (t) cc_final: 0.8031 (p) REVERT: B 9 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7496 (tt) REVERT: B 54 ILE cc_start: 0.8123 (pt) cc_final: 0.7892 (mt) REVERT: E 31 LYS cc_start: 0.7976 (mttt) cc_final: 0.7633 (mmmt) REVERT: G 8 ASP cc_start: 0.6350 (p0) cc_final: 0.6150 (p0) REVERT: H 7 GLU cc_start: 0.6316 (mt-10) cc_final: 0.5566 (mp0) REVERT: L 16 LEU cc_start: 0.5653 (tp) cc_final: 0.5402 (tp) REVERT: L 39 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.7887 (pt) REVERT: L 58 ASP cc_start: 0.6705 (t70) cc_final: 0.6399 (t70) REVERT: L 64 ILE cc_start: 0.8457 (tt) cc_final: 0.8051 (tp) REVERT: M 387 PHE cc_start: 0.7532 (t80) cc_final: 0.7154 (t80) REVERT: M 630 TRP cc_start: 0.8461 (OUTLIER) cc_final: 0.7996 (t60) REVERT: P 22 MET cc_start: 0.8271 (mmm) cc_final: 0.8055 (mmp) REVERT: P 27 HIS cc_start: 0.9133 (OUTLIER) cc_final: 0.8928 (m90) REVERT: Q 55 ARG cc_start: 0.7014 (ttm110) cc_final: 0.6538 (mtp180) REVERT: S 15 LYS cc_start: 0.7257 (ttmm) cc_final: 0.6938 (tptt) REVERT: U 46 LEU cc_start: 0.8121 (tt) cc_final: 0.7190 (mt) REVERT: V 25 LEU cc_start: 0.6215 (OUTLIER) cc_final: 0.5872 (mm) REVERT: W 13 GLN cc_start: 0.6075 (OUTLIER) cc_final: 0.5709 (tm-30) REVERT: W 55 ARG cc_start: 0.6570 (ttp-170) cc_final: 0.6174 (ttm170) REVERT: Y 17 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.7918 (t80) REVERT: C 122 HIS cc_start: 0.7327 (OUTLIER) cc_final: 0.6716 (m-70) REVERT: C 145 MET cc_start: 0.8371 (mmt) cc_final: 0.8088 (mmt) REVERT: C 229 MET cc_start: 0.8879 (mmt) cc_final: 0.8526 (mmt) outliers start: 51 outliers final: 27 residues processed: 345 average time/residue: 0.3865 time to fit residues: 212.4505 Evaluate side-chains 312 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 277 time to evaluate : 3.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 7 residue 33 SER Chi-restraints excluded: chain 9 residue 15 SER Chi-restraints excluded: chain 9 residue 18 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain K residue 7 ASN Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 304 ILE Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 449 VAL Chi-restraints excluded: chain M residue 493 ASN Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 27 HIS Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain W residue 13 GLN Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain Y residue 17 PHE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 312 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 103 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 186 optimal weight: 8.9990 chunk 191 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 159 optimal weight: 9.9990 chunk 195 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 22 GLN B 13 GLN C 87 GLN C 135 ASN Z 58 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.113729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.092663 restraints weight = 41002.997| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.52 r_work: 0.3037 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.295 23298 Z= 0.208 Angle : 0.963 19.573 32512 Z= 0.360 Chirality : 0.044 0.238 3328 Planarity : 0.005 0.081 3826 Dihedral : 18.472 179.716 4007 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.97 % Allowed : 16.40 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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: 1.79 (0.18), residues: 2193 helix: 2.87 (0.13), residues: 1355 sheet: None (None), residues: 0 loop : -1.85 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 38 HIS 0.008 0.002 HIS L 192 PHE 0.025 0.002 PHE M 519 TYR 0.024 0.002 TYR M 424 ARG 0.006 0.001 ARG 1 40 Details of bonding type rmsd hydrogen bonds : bond 0.06652 ( 1114) hydrogen bonds : angle 3.54918 ( 3276) covalent geometry : bond 0.00527 (23233) covalent geometry : angle 0.96285 (32512) Misc. bond : bond 0.06320 ( 65) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 279 time to evaluate : 2.112 Fit side-chains REVERT: 0 15 LYS cc_start: 0.8079 (tppt) cc_final: 0.7333 (tptp) REVERT: 4 9 LEU cc_start: 0.7728 (mt) cc_final: 0.7313 (tp) REVERT: 6 15 LYS cc_start: 0.8047 (mttt) cc_final: 0.7710 (mmtt) REVERT: 6 28 ILE cc_start: 0.8382 (mt) cc_final: 0.8120 (mm) REVERT: 8 41 VAL cc_start: 0.8636 (t) cc_final: 0.8218 (p) REVERT: E 31 LYS cc_start: 0.7996 (mttt) cc_final: 0.7639 (mmmt) REVERT: G 8 ASP cc_start: 0.6443 (p0) cc_final: 0.6243 (p0) REVERT: H 7 GLU cc_start: 0.6277 (mt-10) cc_final: 0.5740 (mp0) REVERT: J 7 GLU cc_start: 0.6749 (mt-10) cc_final: 0.6426 (mt-10) REVERT: L 16 LEU cc_start: 0.5603 (tp) cc_final: 0.5364 (tp) REVERT: L 64 ILE cc_start: 0.8649 (tt) cc_final: 0.8294 (tp) REVERT: L 253 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7552 (mm) REVERT: M 387 PHE cc_start: 0.7588 (t80) cc_final: 0.7249 (t80) REVERT: M 551 LYS cc_start: 0.6551 (mmtt) cc_final: 0.6311 (tmtt) REVERT: Q 55 ARG cc_start: 0.7243 (ttm110) cc_final: 0.6677 (mtp180) REVERT: U 41 VAL cc_start: 0.8456 (t) cc_final: 0.8154 (p) REVERT: V 25 LEU cc_start: 0.5975 (OUTLIER) cc_final: 0.5643 (mm) REVERT: W 38 ILE cc_start: 0.7156 (OUTLIER) cc_final: 0.6930 (mp) REVERT: Y 17 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.7590 (t80) REVERT: C 87 GLN cc_start: 0.7523 (mp10) cc_final: 0.7147 (mp-120) REVERT: C 122 HIS cc_start: 0.7322 (OUTLIER) cc_final: 0.6649 (m-70) REVERT: C 229 MET cc_start: 0.8929 (mmt) cc_final: 0.8538 (mmt) outliers start: 76 outliers final: 52 residues processed: 336 average time/residue: 0.2929 time to fit residues: 159.3810 Evaluate side-chains 328 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 271 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 3 residue 38 TRP Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 5 residue 24 LEU Chi-restraints excluded: chain 6 residue 10 VAL Chi-restraints excluded: chain 6 residue 54 ILE Chi-restraints excluded: chain 7 residue 14 VAL Chi-restraints excluded: chain 7 residue 33 SER Chi-restraints excluded: chain 8 residue 10 VAL Chi-restraints excluded: chain 9 residue 18 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain K residue 7 ASN Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 304 ILE Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain M residue 449 VAL Chi-restraints excluded: chain M residue 493 ASN Chi-restraints excluded: chain M residue 613 LEU Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 47 CYS Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain W residue 10 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 38 ILE Chi-restraints excluded: chain W residue 44 HIS Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain Y residue 17 PHE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain Z residue 58 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 182 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 chunk 114 optimal weight: 0.0270 chunk 65 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 overall best weight: 3.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 7 ASN K 7 ASN U 19 ASN Z 58 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.115673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.095576 restraints weight = 40354.688| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.31 r_work: 0.3070 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.297 23298 Z= 0.167 Angle : 0.874 16.833 32512 Z= 0.328 Chirality : 0.042 0.224 3328 Planarity : 0.005 0.102 3826 Dihedral : 17.995 179.668 4007 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.03 % Allowed : 17.28 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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 (0.18), residues: 2193 helix: 3.01 (0.13), residues: 1353 sheet: None (None), residues: 0 loop : -1.86 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 38 HIS 0.006 0.001 HIS L 192 PHE 0.016 0.001 PHE M 519 TYR 0.018 0.002 TYR M 424 ARG 0.004 0.000 ARG 1 40 Details of bonding type rmsd hydrogen bonds : bond 0.06011 ( 1114) hydrogen bonds : angle 3.44408 ( 3276) covalent geometry : bond 0.00417 (23233) covalent geometry : angle 0.87358 (32512) Misc. bond : bond 0.06246 ( 65) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 287 time to evaluate : 2.370 Fit side-chains REVERT: 0 15 LYS cc_start: 0.8060 (tppt) cc_final: 0.7320 (tptp) REVERT: 4 9 LEU cc_start: 0.7813 (mt) cc_final: 0.7385 (tp) REVERT: 6 15 LYS cc_start: 0.8045 (mttt) cc_final: 0.7691 (mmtt) REVERT: 6 28 ILE cc_start: 0.8370 (mt) cc_final: 0.8117 (mm) REVERT: 8 41 VAL cc_start: 0.8570 (t) cc_final: 0.8163 (p) REVERT: E 31 LYS cc_start: 0.7957 (mttt) cc_final: 0.7627 (mmmt) REVERT: G 8 ASP cc_start: 0.6494 (p0) cc_final: 0.6266 (p0) REVERT: H 7 GLU cc_start: 0.6265 (mt-10) cc_final: 0.5791 (mp0) REVERT: J 7 GLU cc_start: 0.6707 (mt-10) cc_final: 0.6379 (mt-10) REVERT: L 16 LEU cc_start: 0.5444 (tp) cc_final: 0.5239 (tp) REVERT: L 58 ASP cc_start: 0.6822 (t70) cc_final: 0.6498 (t70) REVERT: L 64 ILE cc_start: 0.8657 (tt) cc_final: 0.8306 (tp) REVERT: L 253 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7601 (mm) REVERT: M 357 HIS cc_start: 0.7672 (OUTLIER) cc_final: 0.6709 (t70) REVERT: M 387 PHE cc_start: 0.7574 (t80) cc_final: 0.7214 (t80) REVERT: Q 55 ARG cc_start: 0.7184 (ttm110) cc_final: 0.6678 (mtp180) REVERT: U 13 GLN cc_start: 0.7002 (tt0) cc_final: 0.6791 (tt0) REVERT: V 17 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7228 (tp) REVERT: V 25 LEU cc_start: 0.6094 (OUTLIER) cc_final: 0.5765 (mm) REVERT: W 38 ILE cc_start: 0.7083 (OUTLIER) cc_final: 0.6857 (mp) REVERT: Y 17 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7706 (t80) REVERT: C 87 GLN cc_start: 0.7608 (mp10) cc_final: 0.7406 (mp-120) REVERT: C 122 HIS cc_start: 0.7190 (OUTLIER) cc_final: 0.6495 (m-70) REVERT: C 229 MET cc_start: 0.8932 (mmt) cc_final: 0.8558 (mmt) outliers start: 58 outliers final: 46 residues processed: 330 average time/residue: 0.3395 time to fit residues: 178.2051 Evaluate side-chains 330 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 277 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 3 residue 38 TRP Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 6 residue 54 ILE Chi-restraints excluded: chain 7 residue 33 SER Chi-restraints excluded: chain 9 residue 18 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain K residue 7 ASN Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 304 ILE Chi-restraints excluded: chain L residue 308 VAL Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 357 HIS Chi-restraints excluded: chain M residue 409 LEU Chi-restraints excluded: chain M residue 449 VAL Chi-restraints excluded: chain M residue 493 ASN Chi-restraints excluded: chain M residue 613 LEU Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 38 ILE Chi-restraints excluded: chain W residue 44 HIS Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain Y residue 17 PHE Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 312 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 77 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 192 optimal weight: 20.0000 chunk 161 optimal weight: 0.5980 chunk 150 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 121 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.117280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.096776 restraints weight = 40148.992| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.45 r_work: 0.3109 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.273 23298 Z= 0.133 Angle : 0.829 16.682 32512 Z= 0.315 Chirality : 0.039 0.212 3328 Planarity : 0.004 0.101 3826 Dihedral : 17.757 179.718 4007 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.08 % Allowed : 17.13 % Favored : 79.79 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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: 2.19 (0.18), residues: 2193 helix: 3.28 (0.13), residues: 1350 sheet: None (None), residues: 0 loop : -1.84 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 552 HIS 0.006 0.001 HIS M 525 PHE 0.014 0.001 PHE L 185 TYR 0.017 0.001 TYR O 34 ARG 0.004 0.000 ARG 1 40 Details of bonding type rmsd hydrogen bonds : bond 0.05213 ( 1114) hydrogen bonds : angle 3.31203 ( 3276) covalent geometry : bond 0.00318 (23233) covalent geometry : angle 0.82947 (32512) Misc. bond : bond 0.04946 ( 65) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 291 time to evaluate : 2.311 Fit side-chains REVERT: 4 9 LEU cc_start: 0.7881 (mt) cc_final: 0.7450 (tp) REVERT: 6 15 LYS cc_start: 0.7965 (mttt) cc_final: 0.7665 (mmtt) REVERT: 6 28 ILE cc_start: 0.8305 (mt) cc_final: 0.8042 (mm) REVERT: 8 41 VAL cc_start: 0.8472 (t) cc_final: 0.8089 (p) REVERT: B 54 ILE cc_start: 0.8058 (pt) cc_final: 0.7801 (mt) REVERT: D 4 ARG cc_start: 0.4618 (ttm-80) cc_final: 0.4279 (ttm170) REVERT: D 18 LEU cc_start: 0.8817 (tp) cc_final: 0.8609 (tt) REVERT: E 31 LYS cc_start: 0.7953 (mttt) cc_final: 0.7643 (mmmt) REVERT: G 8 ASP cc_start: 0.6396 (p0) cc_final: 0.6142 (p0) REVERT: H 7 GLU cc_start: 0.6271 (mt-10) cc_final: 0.5627 (mp0) REVERT: L 16 LEU cc_start: 0.5433 (tp) cc_final: 0.5231 (tp) REVERT: L 58 ASP cc_start: 0.6683 (t70) cc_final: 0.6411 (t70) REVERT: L 64 ILE cc_start: 0.8634 (tt) cc_final: 0.8286 (tp) REVERT: L 253 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7494 (mm) REVERT: M 357 HIS cc_start: 0.7621 (OUTLIER) cc_final: 0.6704 (t70) REVERT: M 387 PHE cc_start: 0.7578 (t80) cc_final: 0.7240 (t80) REVERT: M 519 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8281 (t80) REVERT: M 630 TRP cc_start: 0.8468 (OUTLIER) cc_final: 0.7983 (t60) REVERT: Q 55 ARG cc_start: 0.7157 (ttm110) cc_final: 0.6639 (mtp180) REVERT: U 46 LEU cc_start: 0.8101 (tt) cc_final: 0.7160 (mt) REVERT: V 25 LEU cc_start: 0.6195 (OUTLIER) cc_final: 0.5869 (mm) REVERT: W 38 ILE cc_start: 0.7110 (OUTLIER) cc_final: 0.6896 (mp) REVERT: Y 17 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7759 (t80) REVERT: C 98 THR cc_start: 0.6865 (p) cc_final: 0.6624 (p) REVERT: C 122 HIS cc_start: 0.7227 (OUTLIER) cc_final: 0.6590 (m-70) REVERT: C 229 MET cc_start: 0.8910 (mmt) cc_final: 0.8561 (mmt) REVERT: C 268 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8343 (tttt) REVERT: C 286 MET cc_start: 0.7955 (mtt) cc_final: 0.7608 (mtt) outliers start: 59 outliers final: 44 residues processed: 333 average time/residue: 0.3231 time to fit residues: 173.2998 Evaluate side-chains 326 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 273 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 3 residue 38 TRP Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 7 residue 33 SER Chi-restraints excluded: chain 8 residue 10 VAL Chi-restraints excluded: chain 9 residue 17 LEU Chi-restraints excluded: chain 9 residue 18 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 304 ILE Chi-restraints excluded: chain L residue 308 VAL Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 357 HIS Chi-restraints excluded: chain M residue 409 LEU Chi-restraints excluded: chain M residue 449 VAL Chi-restraints excluded: chain M residue 493 ASN Chi-restraints excluded: chain M residue 519 PHE Chi-restraints excluded: chain M residue 613 LEU Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 47 CYS Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 38 ILE Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain Y residue 17 PHE Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 268 LYS Chi-restraints excluded: chain C residue 312 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 13 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 32 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 chunk 144 optimal weight: 5.9990 chunk 186 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 194 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.118554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.097840 restraints weight = 39938.098| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.44 r_work: 0.3128 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.365 23298 Z= 0.125 Angle : 0.796 15.693 32512 Z= 0.300 Chirality : 0.039 0.197 3328 Planarity : 0.004 0.096 3826 Dihedral : 17.245 179.738 4007 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.98 % Allowed : 17.55 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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: 2.35 (0.18), residues: 2193 helix: 3.36 (0.13), residues: 1353 sheet: None (None), residues: 0 loop : -1.70 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 38 HIS 0.005 0.001 HIS M 525 PHE 0.013 0.001 PHE L 185 TYR 0.017 0.001 TYR O 34 ARG 0.003 0.000 ARG 1 40 Details of bonding type rmsd hydrogen bonds : bond 0.04726 ( 1114) hydrogen bonds : angle 3.23891 ( 3276) covalent geometry : bond 0.00301 (23233) covalent geometry : angle 0.79567 (32512) Misc. bond : bond 0.06286 ( 65) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 284 time to evaluate : 2.116 Fit side-chains REVERT: 4 9 LEU cc_start: 0.7843 (mt) cc_final: 0.7426 (tp) REVERT: 6 15 LYS cc_start: 0.7966 (mttt) cc_final: 0.7639 (mmtt) REVERT: 6 28 ILE cc_start: 0.8245 (mt) cc_final: 0.8003 (mm) REVERT: D 4 ARG cc_start: 0.4662 (ttm-80) cc_final: 0.4333 (ttm170) REVERT: E 31 LYS cc_start: 0.7954 (mttt) cc_final: 0.7639 (mmmt) REVERT: G 8 ASP cc_start: 0.6439 (p0) cc_final: 0.6192 (p0) REVERT: G 13 GLN cc_start: 0.6522 (OUTLIER) cc_final: 0.6050 (pm20) REVERT: L 64 ILE cc_start: 0.8603 (tt) cc_final: 0.8264 (tp) REVERT: L 253 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7481 (mm) REVERT: M 357 HIS cc_start: 0.7541 (OUTLIER) cc_final: 0.6607 (t70) REVERT: M 387 PHE cc_start: 0.7582 (t80) cc_final: 0.7229 (t80) REVERT: M 519 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8265 (t80) REVERT: M 630 TRP cc_start: 0.8458 (OUTLIER) cc_final: 0.8045 (t60) REVERT: Q 55 ARG cc_start: 0.7217 (ttm110) cc_final: 0.6677 (mtp180) REVERT: U 46 LEU cc_start: 0.8107 (tt) cc_final: 0.7163 (mt) REVERT: V 25 LEU cc_start: 0.6257 (OUTLIER) cc_final: 0.5941 (mm) REVERT: W 38 ILE cc_start: 0.7052 (OUTLIER) cc_final: 0.6826 (mp) REVERT: Y 17 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.7788 (t80) REVERT: C 98 THR cc_start: 0.6739 (p) cc_final: 0.6520 (p) REVERT: C 122 HIS cc_start: 0.7304 (OUTLIER) cc_final: 0.6655 (m-70) REVERT: C 229 MET cc_start: 0.8892 (mmt) cc_final: 0.8507 (mmt) REVERT: C 268 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8362 (tttt) outliers start: 57 outliers final: 43 residues processed: 322 average time/residue: 0.3112 time to fit residues: 160.2952 Evaluate side-chains 322 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 269 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 6 residue 10 VAL Chi-restraints excluded: chain 7 residue 33 SER Chi-restraints excluded: chain 8 residue 10 VAL Chi-restraints excluded: chain 9 residue 17 LEU Chi-restraints excluded: chain 9 residue 18 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain K residue 7 ASN Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 304 ILE Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 357 HIS Chi-restraints excluded: chain M residue 449 VAL Chi-restraints excluded: chain M residue 493 ASN Chi-restraints excluded: chain M residue 519 PHE Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 47 CYS Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 38 ILE Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain Y residue 17 PHE Chi-restraints excluded: chain C residue 31 MET Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 268 LYS Chi-restraints excluded: chain C residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 20 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 18 optimal weight: 0.3980 chunk 125 optimal weight: 8.9990 chunk 198 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 199 optimal weight: 9.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.114929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.095263 restraints weight = 40308.106| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.26 r_work: 0.3058 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.313 23298 Z= 0.191 Angle : 0.900 17.905 32512 Z= 0.348 Chirality : 0.043 0.239 3328 Planarity : 0.005 0.094 3826 Dihedral : 17.429 179.695 4007 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.98 % Allowed : 17.70 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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: 1.97 (0.18), residues: 2193 helix: 3.02 (0.13), residues: 1353 sheet: None (None), residues: 0 loop : -1.78 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 38 HIS 0.007 0.001 HIS L 192 PHE 0.019 0.002 PHE M 519 TYR 0.021 0.002 TYR M 424 ARG 0.003 0.000 ARG P 4 Details of bonding type rmsd hydrogen bonds : bond 0.06224 ( 1114) hydrogen bonds : angle 3.47831 ( 3276) covalent geometry : bond 0.00480 (23233) covalent geometry : angle 0.89993 (32512) Misc. bond : bond 0.06094 ( 65) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 283 time to evaluate : 2.057 Fit side-chains REVERT: 2 37 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.7029 (tt) REVERT: 4 9 LEU cc_start: 0.7820 (mt) cc_final: 0.7411 (tp) REVERT: 6 15 LYS cc_start: 0.8004 (mttt) cc_final: 0.7702 (mmtt) REVERT: 6 28 ILE cc_start: 0.8370 (mt) cc_final: 0.8121 (mm) REVERT: 9 16 THR cc_start: 0.8388 (m) cc_final: 0.8158 (m) REVERT: B 54 ILE cc_start: 0.8097 (pt) cc_final: 0.7800 (mt) REVERT: B 55 ARG cc_start: 0.7503 (ttp-170) cc_final: 0.7008 (mtm180) REVERT: D 4 ARG cc_start: 0.4888 (ttm-80) cc_final: 0.4558 (ttm170) REVERT: D 18 LEU cc_start: 0.8932 (tp) cc_final: 0.8701 (tt) REVERT: D 37 ASN cc_start: 0.7329 (t0) cc_final: 0.6982 (t0) REVERT: E 31 LYS cc_start: 0.7994 (mttt) cc_final: 0.7668 (mmmt) REVERT: G 8 ASP cc_start: 0.6478 (p0) cc_final: 0.6218 (p0) REVERT: H 7 GLU cc_start: 0.6691 (mm-30) cc_final: 0.6428 (tp30) REVERT: I 18 PHE cc_start: 0.8205 (m-80) cc_final: 0.7963 (m-80) REVERT: J 7 GLU cc_start: 0.6770 (mt-10) cc_final: 0.6358 (tt0) REVERT: L 64 ILE cc_start: 0.8744 (tt) cc_final: 0.8422 (tp) REVERT: L 253 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7616 (mm) REVERT: M 357 HIS cc_start: 0.7571 (OUTLIER) cc_final: 0.6644 (t70) REVERT: M 387 PHE cc_start: 0.7667 (t80) cc_final: 0.7333 (t80) REVERT: M 519 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8439 (t80) REVERT: Q 55 ARG cc_start: 0.7235 (ttm110) cc_final: 0.6688 (mtp180) REVERT: U 41 VAL cc_start: 0.8306 (t) cc_final: 0.8056 (p) REVERT: V 17 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7322 (tp) REVERT: V 25 LEU cc_start: 0.6177 (OUTLIER) cc_final: 0.5860 (mm) REVERT: W 38 ILE cc_start: 0.7225 (OUTLIER) cc_final: 0.6995 (mp) REVERT: Y 17 PHE cc_start: 0.8377 (OUTLIER) cc_final: 0.7685 (t80) REVERT: C 98 THR cc_start: 0.6850 (p) cc_final: 0.6485 (p) REVERT: C 122 HIS cc_start: 0.7456 (OUTLIER) cc_final: 0.6724 (m-70) REVERT: C 229 MET cc_start: 0.8918 (mmt) cc_final: 0.8554 (mmt) REVERT: C 268 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8393 (tttt) REVERT: C 286 MET cc_start: 0.8153 (mtt) cc_final: 0.7809 (mtt) outliers start: 57 outliers final: 44 residues processed: 324 average time/residue: 0.3230 time to fit residues: 167.5315 Evaluate side-chains 328 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 274 time to evaluate : 2.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 3 residue 38 TRP Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 6 residue 10 VAL Chi-restraints excluded: chain 7 residue 33 SER Chi-restraints excluded: chain 8 residue 10 VAL Chi-restraints excluded: chain 9 residue 18 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 304 ILE Chi-restraints excluded: chain L residue 308 VAL Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 357 HIS Chi-restraints excluded: chain M residue 449 VAL Chi-restraints excluded: chain M residue 493 ASN Chi-restraints excluded: chain M residue 519 PHE Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 47 CYS Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 38 ILE Chi-restraints excluded: chain W residue 44 HIS Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain Y residue 17 PHE Chi-restraints excluded: chain C residue 31 MET Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 268 LYS Chi-restraints excluded: chain C residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 128 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 176 optimal weight: 0.7980 chunk 98 optimal weight: 0.1980 chunk 104 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 127 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 79 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.119761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.099367 restraints weight = 40062.153| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.42 r_work: 0.3146 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.276 23298 Z= 0.119 Angle : 0.761 15.754 32512 Z= 0.292 Chirality : 0.038 0.189 3328 Planarity : 0.004 0.103 3826 Dihedral : 16.712 179.790 4007 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.51 % Allowed : 18.90 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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: 2.50 (0.19), residues: 2193 helix: 3.46 (0.13), residues: 1349 sheet: None (None), residues: 0 loop : -1.58 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 63 HIS 0.006 0.001 HIS M 525 PHE 0.011 0.001 PHE L 185 TYR 0.016 0.001 TYR G 34 ARG 0.003 0.000 ARG P 40 Details of bonding type rmsd hydrogen bonds : bond 0.04384 ( 1114) hydrogen bonds : angle 3.20867 ( 3276) covalent geometry : bond 0.00268 (23233) covalent geometry : angle 0.76064 (32512) Misc. bond : bond 0.04775 ( 65) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12782.81 seconds wall clock time: 222 minutes 26.63 seconds (13346.63 seconds total)