Starting phenix.real_space_refine on Thu Sep 18 20:43:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mko_48332/09_2025/9mko_48332_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mko_48332/09_2025/9mko_48332.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mko_48332/09_2025/9mko_48332_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mko_48332/09_2025/9mko_48332_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mko_48332/09_2025/9mko_48332.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mko_48332/09_2025/9mko_48332.map" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.090 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 134 5.16 5 C 12336 2.51 5 N 3288 2.21 5 O 3817 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19575 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 1244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1244 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 157} Chain: "B" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1279 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 172} Chain: "C" Number of atoms: 1244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1244 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 157} Chain: "D" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1279 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 172} Chain: "F" Number of atoms: 1244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1244 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 157} Chain: "G" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1279 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 172} Chain: "I" Number of atoms: 1244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1244 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 157} Chain: "J" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1279 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 172} Chain: "L" Number of atoms: 1244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1244 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 157} Chain: "M" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1279 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 172} Chain: "O" Number of atoms: 1244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1244 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 157} Chain: "Q" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1279 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 172} Chain: "a" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1391 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Chain breaks: 2 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'ARG:plan': 1, 'PHE:plan': 2, 'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "b" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1756 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 5, 'GLU:plan': 5, 'ASN:plan1': 3, 'PHE:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 85 Chain: "A" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PEB': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'PEB': 2, 'PUB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PEB': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'PEB': 2, 'PUB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PEB': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'PEB': 2, 'PUB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PEB': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'PEB': 2, 'PUB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PEB': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'PEB': 2, 'PUB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PEB': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'PEB': 2, 'PUB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.83, per 1000 atoms: 0.25 Number of scatterers: 19575 At special positions: 0 Unit cell: (109.61, 132.89, 191.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 134 16.00 O 3817 8.00 N 3288 7.00 C 12336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS a 23 " - pdb=" SG CYS a 87 " distance=2.03 Simple disulfide: pdb=" SG CYS a 132 " - pdb=" SG CYS a 182 " distance=2.03 Simple disulfide: pdb=" SG CYS a 157 " - pdb=" SG CYS b 170 " distance=2.32 Simple disulfide: pdb=" SG CYS b 24 " - pdb=" SG CYS b 92 " distance=2.03 Simple disulfide: pdb=" SG CYS b 144 " - pdb=" SG CYS b 209 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4610 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 9 sheets defined 71.7% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 removed outlier: 3.593A pdb=" N ALA A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 47 removed outlier: 3.522A pdb=" N VAL A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA A 35 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N SER A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A 40 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY A 46 " --> pdb=" O GLU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 63 removed outlier: 3.629A pdb=" N ASP A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 75 through 100 removed outlier: 3.557A pdb=" N VAL A 98 " --> pdb=" O ASN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 109 Processing helix chain 'A' and resid 112 through 121 removed outlier: 3.605A pdb=" N ARG A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 138 removed outlier: 4.053A pdb=" N TYR A 127 " --> pdb=" O PRO A 123 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 130 " --> pdb=" O SER A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 164 removed outlier: 3.696A pdb=" N LEU A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 14 removed outlier: 3.578A pdb=" N VAL B 8 " --> pdb=" O ALA B 4 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 14 " --> pdb=" O VAL B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 33 removed outlier: 3.982A pdb=" N ALA B 26 " --> pdb=" O SER B 22 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU B 27 " --> pdb=" O ASP B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 47 removed outlier: 3.522A pdb=" N ALA B 40 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 41 " --> pdb=" O ARG B 37 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 63 Processing helix chain 'B' and resid 64 through 67 removed outlier: 3.652A pdb=" N ILE B 67 " --> pdb=" O PRO B 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 64 through 67' Processing helix chain 'B' and resid 75 through 100 Processing helix chain 'B' and resid 102 through 109 Processing helix chain 'B' and resid 112 through 121 Processing helix chain 'B' and resid 123 through 143 Processing helix chain 'B' and resid 158 through 176 Processing helix chain 'C' and resid 3 through 15 removed outlier: 3.615A pdb=" N ALA C 15 " --> pdb=" O ALA C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 47 removed outlier: 3.651A pdb=" N SER C 26 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL C 27 " --> pdb=" O ASP C 23 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY C 29 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALA C 35 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N SER C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU C 39 " --> pdb=" O ALA C 35 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C 41 " --> pdb=" O ARG C 37 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 63 removed outlier: 3.503A pdb=" N LYS C 53 " --> pdb=" O GLU C 49 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR C 63 " --> pdb=" O CYS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 68 Processing helix chain 'C' and resid 75 through 100 Processing helix chain 'C' and resid 102 through 109 Processing helix chain 'C' and resid 112 through 120 removed outlier: 3.524A pdb=" N ARG C 118 " --> pdb=" O ARG C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 138 Processing helix chain 'C' and resid 145 through 164 removed outlier: 3.607A pdb=" N LEU C 163 " --> pdb=" O VAL C 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 14 removed outlier: 3.583A pdb=" N VAL D 8 " --> pdb=" O ALA D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 33 removed outlier: 3.508A pdb=" N ALA D 26 " --> pdb=" O SER D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 47 removed outlier: 3.761A pdb=" N SER D 43 " --> pdb=" O ASP D 39 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 63 removed outlier: 3.689A pdb=" N SER D 53 " --> pdb=" O SER D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 67 Processing helix chain 'D' and resid 75 through 100 Processing helix chain 'D' and resid 102 through 109 removed outlier: 3.582A pdb=" N CYS D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 121 Processing helix chain 'D' and resid 123 through 143 Processing helix chain 'D' and resid 158 through 176 Processing helix chain 'F' and resid 3 through 16 removed outlier: 3.621A pdb=" N THR F 8 " --> pdb=" O VAL F 4 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA F 15 " --> pdb=" O ALA F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 46 removed outlier: 4.188A pdb=" N ALA F 35 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N SER F 36 " --> pdb=" O GLN F 32 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU F 39 " --> pdb=" O ALA F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 63 removed outlier: 3.698A pdb=" N ASP F 57 " --> pdb=" O LYS F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 68 Processing helix chain 'F' and resid 75 through 100 Processing helix chain 'F' and resid 102 through 109 Processing helix chain 'F' and resid 112 through 121 Processing helix chain 'F' and resid 123 through 138 removed outlier: 4.263A pdb=" N TYR F 127 " --> pdb=" O PRO F 123 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA F 130 " --> pdb=" O SER F 126 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE F 131 " --> pdb=" O TYR F 127 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU F 138 " --> pdb=" O THR F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 164 removed outlier: 3.529A pdb=" N VAL F 150 " --> pdb=" O ALA F 146 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA F 155 " --> pdb=" O GLU F 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 14 removed outlier: 3.603A pdb=" N VAL G 9 " --> pdb=" O PHE G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 33 removed outlier: 3.645A pdb=" N THR G 29 " --> pdb=" O GLN G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 47 Processing helix chain 'G' and resid 47 through 63 removed outlier: 3.581A pdb=" N VAL G 52 " --> pdb=" O ALA G 48 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER G 53 " --> pdb=" O SER G 49 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU G 62 " --> pdb=" O GLY G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 67 removed outlier: 3.540A pdb=" N ILE G 67 " --> pdb=" O PRO G 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 64 through 67' Processing helix chain 'G' and resid 75 through 100 Processing helix chain 'G' and resid 102 through 109 Processing helix chain 'G' and resid 112 through 121 Processing helix chain 'G' and resid 123 through 143 Processing helix chain 'G' and resid 158 through 176 Processing helix chain 'I' and resid 3 through 16 removed outlier: 3.573A pdb=" N THR I 8 " --> pdb=" O VAL I 4 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA I 15 " --> pdb=" O ALA I 11 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 47 removed outlier: 3.820A pdb=" N SER I 26 " --> pdb=" O SER I 22 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL I 27 " --> pdb=" O ASP I 23 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA I 35 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N SER I 36 " --> pdb=" O GLN I 32 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG I 37 " --> pdb=" O ARG I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 63 removed outlier: 3.618A pdb=" N LYS I 53 " --> pdb=" O GLU I 49 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR I 63 " --> pdb=" O CYS I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 68 Processing helix chain 'I' and resid 75 through 100 Processing helix chain 'I' and resid 102 through 109 removed outlier: 3.521A pdb=" N GLU I 107 " --> pdb=" O GLY I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 120 Processing helix chain 'I' and resid 123 through 138 removed outlier: 4.285A pdb=" N TYR I 127 " --> pdb=" O PRO I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 164 removed outlier: 3.554A pdb=" N ALA I 149 " --> pdb=" O SER I 145 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL I 150 " --> pdb=" O ALA I 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 14 removed outlier: 3.663A pdb=" N VAL J 8 " --> pdb=" O ALA J 4 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL J 9 " --> pdb=" O PHE J 5 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER J 14 " --> pdb=" O VAL J 10 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 33 Processing helix chain 'J' and resid 33 through 47 removed outlier: 3.721A pdb=" N SER J 43 " --> pdb=" O ASP J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 62 removed outlier: 3.568A pdb=" N GLU J 62 " --> pdb=" O GLY J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 67 Processing helix chain 'J' and resid 75 through 100 Processing helix chain 'J' and resid 102 through 109 Processing helix chain 'J' and resid 112 through 121 Processing helix chain 'J' and resid 123 through 143 removed outlier: 3.664A pdb=" N THR J 127 " --> pdb=" O PRO J 123 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL J 128 " --> pdb=" O THR J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 176 removed outlier: 3.562A pdb=" N ILE J 176 " --> pdb=" O VAL J 172 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 16 removed outlier: 3.650A pdb=" N ALA L 15 " --> pdb=" O ALA L 11 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 47 removed outlier: 3.631A pdb=" N VAL L 27 " --> pdb=" O ASP L 23 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN L 30 " --> pdb=" O SER L 26 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE L 31 " --> pdb=" O VAL L 27 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA L 35 " --> pdb=" O ILE L 31 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N SER L 36 " --> pdb=" O GLN L 32 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG L 37 " --> pdb=" O ARG L 33 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU L 39 " --> pdb=" O ALA L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 63 removed outlier: 3.524A pdb=" N PHE L 60 " --> pdb=" O GLY L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 68 Processing helix chain 'L' and resid 75 through 100 removed outlier: 3.507A pdb=" N ASN L 80 " --> pdb=" O GLN L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 109 Processing helix chain 'L' and resid 112 through 120 removed outlier: 3.662A pdb=" N ARG L 118 " --> pdb=" O ARG L 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 138 removed outlier: 4.172A pdb=" N TYR L 127 " --> pdb=" O PRO L 123 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR L 134 " --> pdb=" O ALA L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 164 Processing helix chain 'M' and resid 3 through 15 removed outlier: 3.756A pdb=" N VAL M 8 " --> pdb=" O ALA M 4 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS M 15 " --> pdb=" O ASN M 11 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 33 removed outlier: 3.619A pdb=" N PHE M 30 " --> pdb=" O ALA M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 33 through 47 removed outlier: 3.641A pdb=" N VAL M 41 " --> pdb=" O ARG M 37 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN M 42 " --> pdb=" O LEU M 38 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN M 47 " --> pdb=" O SER M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 47 through 63 Processing helix chain 'M' and resid 64 through 67 Processing helix chain 'M' and resid 75 through 100 Processing helix chain 'M' and resid 102 through 109 Processing helix chain 'M' and resid 112 through 121 Processing helix chain 'M' and resid 123 through 143 Processing helix chain 'M' and resid 158 through 176 Processing helix chain 'O' and resid 3 through 16 removed outlier: 3.585A pdb=" N ALA O 15 " --> pdb=" O ALA O 11 " (cutoff:3.500A) Processing helix chain 'O' and resid 20 through 47 removed outlier: 3.513A pdb=" N SER O 26 " --> pdb=" O SER O 22 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL O 27 " --> pdb=" O ASP O 23 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN O 30 " --> pdb=" O SER O 26 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA O 35 " --> pdb=" O ILE O 31 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N SER O 36 " --> pdb=" O GLN O 32 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU O 39 " --> pdb=" O ALA O 35 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA O 40 " --> pdb=" O SER O 36 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY O 46 " --> pdb=" O GLU O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 47 through 63 removed outlier: 3.651A pdb=" N VAL O 51 " --> pdb=" O ASN O 47 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE O 60 " --> pdb=" O GLY O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 64 through 68 Processing helix chain 'O' and resid 75 through 100 removed outlier: 3.542A pdb=" N TYR O 83 " --> pdb=" O ILE O 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 102 through 109 Processing helix chain 'O' and resid 112 through 120 removed outlier: 3.523A pdb=" N ARG O 118 " --> pdb=" O ARG O 114 " (cutoff:3.500A) Processing helix chain 'O' and resid 123 through 138 removed outlier: 4.136A pdb=" N TYR O 127 " --> pdb=" O PRO O 123 " (cutoff:3.500A) Processing helix chain 'O' and resid 145 through 164 removed outlier: 3.522A pdb=" N VAL O 150 " --> pdb=" O ALA O 146 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 14 Processing helix chain 'Q' and resid 20 through 33 removed outlier: 3.526A pdb=" N PHE Q 30 " --> pdb=" O ALA Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 47 removed outlier: 3.926A pdb=" N SER Q 43 " --> pdb=" O ASP Q 39 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN Q 47 " --> pdb=" O SER Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 63 Processing helix chain 'Q' and resid 75 through 100 Processing helix chain 'Q' and resid 102 through 109 removed outlier: 3.546A pdb=" N CYS Q 109 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 112 through 121 Processing helix chain 'Q' and resid 123 through 143 removed outlier: 3.687A pdb=" N ARG Q 129 " --> pdb=" O ASN Q 125 " (cutoff:3.500A) Processing helix chain 'Q' and resid 158 through 176 Processing helix chain 'a' and resid 78 through 82 Processing helix chain 'a' and resid 181 through 185 removed outlier: 3.628A pdb=" N ALA a 185 " --> pdb=" O CYS a 182 " (cutoff:3.500A) Processing helix chain 'b' and resid 83 through 87 Processing helix chain 'b' and resid 115 through 119 removed outlier: 4.168A pdb=" N VAL b 119 " --> pdb=" O LEU b 116 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 138 Processing helix chain 'b' and resid 196 through 202 Processing sheet with id=AA1, first strand: chain 'a' and resid 4 through 5 removed outlier: 3.745A pdb=" N GLU a 5 " --> pdb=" O ASN a 24 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN a 24 " --> pdb=" O GLU a 5 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N SER a 19 " --> pdb=" O ILE a 74 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE a 74 " --> pdb=" O SER a 19 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR a 69 " --> pdb=" O ASP a 64 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP a 64 " --> pdb=" O TYR a 69 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR a 71 " --> pdb=" O ALA a 62 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA a 62 " --> pdb=" O THR a 71 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS a 60 " --> pdb=" O HIS a 73 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU a 59 " --> pdb=" O ASN a 56 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN a 56 " --> pdb=" O LEU a 59 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS a 54 " --> pdb=" O SER a 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 43 through 49 removed outlier: 6.529A pdb=" N TRP a 34 " --> pdb=" O LEU a 46 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N TYR a 48 " --> pdb=" O VAL a 32 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N VAL a 32 " --> pdb=" O TYR a 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 43 through 49 removed outlier: 6.529A pdb=" N TRP a 34 " --> pdb=" O LEU a 46 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N TYR a 48 " --> pdb=" O VAL a 32 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N VAL a 32 " --> pdb=" O TYR a 48 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY a 83 " --> pdb=" O LEU a 105 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 157 through 161 removed outlier: 3.841A pdb=" N SER a 170 " --> pdb=" O CYS a 157 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU a 159 " --> pdb=" O SER a 168 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER a 168 " --> pdb=" O LEU a 159 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE a 166 " --> pdb=" O MET a 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 6 through 8 removed outlier: 3.650A pdb=" N PHE b 6 " --> pdb=" O LYS b 25 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS b 25 " --> pdb=" O PHE b 6 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 12 through 15 removed outlier: 3.933A pdb=" N HIS b 12 " --> pdb=" O ARG b 109 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR b 111 " --> pdb=" O HIS b 12 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU b 113 " --> pdb=" O THR b 14 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LYS b 37 " --> pdb=" O ILE b 46 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ILE b 46 " --> pdb=" O LYS b 37 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N SER b 49 " --> pdb=" O ILE b 56 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 12 through 15 removed outlier: 3.933A pdb=" N HIS b 12 " --> pdb=" O ARG b 109 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR b 111 " --> pdb=" O HIS b 12 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU b 113 " --> pdb=" O THR b 14 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 123 through 126 removed outlier: 3.618A pdb=" N CYS b 144 " --> pdb=" O SER b 191 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER b 191 " --> pdb=" O CYS b 144 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N CYS b 170 " --> pdb=" O ARG b 192 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 163 through 164 removed outlier: 4.055A pdb=" N SER b 157 " --> pdb=" O GLN b 210 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN b 210 " --> pdb=" O SER b 157 " (cutoff:3.500A) 1253 hydrogen bonds defined for protein. 3657 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.20 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5549 1.33 - 1.45: 3394 1.45 - 1.57: 10809 1.57 - 1.69: 1 1.69 - 1.82: 186 Bond restraints: 19939 Sorted by residual: bond pdb=" C1B PEB C 202 " pdb=" CHA PEB C 202 " ideal model delta sigma weight residual 1.441 1.355 0.086 2.00e-02 2.50e+03 1.87e+01 bond pdb=" C1B PEB F 202 " pdb=" CHA PEB F 202 " ideal model delta sigma weight residual 1.441 1.358 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C1B PEB I 201 " pdb=" CHA PEB I 201 " ideal model delta sigma weight residual 1.441 1.358 0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C1B PEB B 202 " pdb=" CHA PEB B 202 " ideal model delta sigma weight residual 1.441 1.359 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C1B PEB L 202 " pdb=" CHA PEB L 202 " ideal model delta sigma weight residual 1.441 1.359 0.082 2.00e-02 2.50e+03 1.67e+01 ... (remaining 19934 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 26194 1.83 - 3.66: 872 3.66 - 5.49: 80 5.49 - 7.32: 22 7.32 - 9.15: 6 Bond angle restraints: 27174 Sorted by residual: angle pdb=" CA ILE A 110 " pdb=" C ILE A 110 " pdb=" O ILE A 110 " ideal model delta sigma weight residual 121.41 117.51 3.90 1.04e+00 9.25e-01 1.41e+01 angle pdb=" C ASP B 39 " pdb=" CA ASP B 39 " pdb=" CB ASP B 39 " ideal model delta sigma weight residual 110.79 105.40 5.39 1.66e+00 3.63e-01 1.05e+01 angle pdb=" CA ASP G 39 " pdb=" CB ASP G 39 " pdb=" CG ASP G 39 " ideal model delta sigma weight residual 112.60 115.55 -2.95 1.00e+00 1.00e+00 8.68e+00 angle pdb=" N ASP B 39 " pdb=" CA ASP B 39 " pdb=" CB ASP B 39 " ideal model delta sigma weight residual 110.12 114.44 -4.32 1.47e+00 4.63e-01 8.65e+00 angle pdb=" CA VAL G 41 " pdb=" C VAL G 41 " pdb=" O VAL G 41 " ideal model delta sigma weight residual 121.27 118.24 3.03 1.04e+00 9.25e-01 8.49e+00 ... (remaining 27169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 10705 17.99 - 35.97: 1705 35.97 - 53.96: 390 53.96 - 71.95: 115 71.95 - 89.93: 46 Dihedral angle restraints: 12961 sinusoidal: 5809 harmonic: 7152 Sorted by residual: dihedral pdb=" CD ARG G 37 " pdb=" NE ARG G 37 " pdb=" CZ ARG G 37 " pdb=" NH1 ARG G 37 " ideal model delta sinusoidal sigma weight residual 0.00 73.55 -73.55 1 1.00e+01 1.00e-02 6.88e+01 dihedral pdb=" CD ARG I 135 " pdb=" NE ARG I 135 " pdb=" CZ ARG I 135 " pdb=" NH1 ARG I 135 " ideal model delta sinusoidal sigma weight residual 0.00 66.20 -66.20 1 1.00e+01 1.00e-02 5.73e+01 dihedral pdb=" CD ARG I 137 " pdb=" NE ARG I 137 " pdb=" CZ ARG I 137 " pdb=" NH1 ARG I 137 " ideal model delta sinusoidal sigma weight residual 0.00 -58.59 58.59 1 1.00e+01 1.00e-02 4.60e+01 ... (remaining 12958 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2390 0.047 - 0.094: 498 0.094 - 0.141: 73 0.141 - 0.188: 14 0.188 - 0.235: 22 Chirality restraints: 2997 Sorted by residual: chirality pdb=" C1D PEB B 202 " pdb=" ND PEB B 202 " pdb=" C2D PEB B 202 " pdb=" CHC PEB B 202 " both_signs ideal model delta sigma weight residual False -2.56 -2.80 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" C1D PEB C 202 " pdb=" ND PEB C 202 " pdb=" C2D PEB C 202 " pdb=" CHC PEB C 202 " both_signs ideal model delta sigma weight residual False -2.56 -2.80 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C1D PEB M 203 " pdb=" ND PEB M 203 " pdb=" C2D PEB M 203 " pdb=" CHC PEB M 203 " both_signs ideal model delta sigma weight residual False -2.56 -2.79 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 2994 not shown) Planarity restraints: 3471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB PEB B 203 " 0.124 2.00e-02 2.50e+03 3.97e-01 3.55e+03 pdb=" C1B PEB B 203 " -0.071 2.00e-02 2.50e+03 pdb=" C2B PEB B 203 " 0.168 2.00e-02 2.50e+03 pdb=" C3B PEB B 203 " -0.142 2.00e-02 2.50e+03 pdb=" C4B PEB B 203 " 0.118 2.00e-02 2.50e+03 pdb=" CAB PEB B 203 " -0.689 2.00e-02 2.50e+03 pdb=" CHA PEB B 203 " -0.532 2.00e-02 2.50e+03 pdb=" CHB PEB B 203 " 0.348 2.00e-02 2.50e+03 pdb=" CMB PEB B 203 " 0.676 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB PEB C 202 " -0.273 2.00e-02 2.50e+03 3.87e-01 3.37e+03 pdb=" C1B PEB C 202 " 0.049 2.00e-02 2.50e+03 pdb=" C2B PEB C 202 " -0.171 2.00e-02 2.50e+03 pdb=" C3B PEB C 202 " 0.112 2.00e-02 2.50e+03 pdb=" C4B PEB C 202 " -0.136 2.00e-02 2.50e+03 pdb=" CAB PEB C 202 " 0.634 2.00e-02 2.50e+03 pdb=" CHA PEB C 202 " 0.618 2.00e-02 2.50e+03 pdb=" CHB PEB C 202 " -0.216 2.00e-02 2.50e+03 pdb=" CMB PEB C 202 " -0.617 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB PEB Q 203 " 0.312 2.00e-02 2.50e+03 3.85e-01 3.34e+03 pdb=" C1B PEB Q 203 " -0.058 2.00e-02 2.50e+03 pdb=" C2B PEB Q 203 " 0.153 2.00e-02 2.50e+03 pdb=" C3B PEB Q 203 " -0.115 2.00e-02 2.50e+03 pdb=" C4B PEB Q 203 " 0.136 2.00e-02 2.50e+03 pdb=" CAB PEB Q 203 " -0.613 2.00e-02 2.50e+03 pdb=" CHA PEB Q 203 " -0.624 2.00e-02 2.50e+03 pdb=" CHB PEB Q 203 " 0.196 2.00e-02 2.50e+03 pdb=" CMB PEB Q 203 " 0.613 2.00e-02 2.50e+03 ... (remaining 3468 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 461 2.71 - 3.25: 19466 3.25 - 3.80: 31014 3.80 - 4.35: 38826 4.35 - 4.90: 64245 Nonbonded interactions: 154012 Sorted by model distance: nonbonded pdb=" OG SER B 147 " pdb=" OE1 GLN B 148 " model vdw 2.158 3.040 nonbonded pdb=" OE2 GLU Q 164 " pdb=" OH TYR Q 168 " model vdw 2.211 3.040 nonbonded pdb=" CG2 ILE C 5 " pdb=" OD2 ASP G 3 " model vdw 2.228 3.460 nonbonded pdb=" OG SER A 26 " pdb=" OG SER O 26 " model vdw 2.247 3.040 nonbonded pdb=" OD1 ASP O 106 " pdb=" OH TYR O 158 " model vdw 2.262 3.040 ... (remaining 154007 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 'A' selection = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' } ncs_group { reference = (chain 'B' and (resid 1 through 176 or resid 202)) selection = (chain 'D' and (resid 1 through 176 or resid 202)) selection = (chain 'G' and (resid 1 through 176 or resid 202)) selection = (chain 'J' and (resid 1 through 176 or resid 202)) selection = (chain 'M' and (resid 1 through 176 or resid 202)) selection = (chain 'Q' and (resid 1 through 176 or resid 202)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 2.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.020 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 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 : 0.007 0.284 19944 Z= 0.339 Angle : 0.732 19.300 27184 Z= 0.350 Chirality : 0.043 0.235 2997 Planarity : 0.028 0.475 3471 Dihedral : 18.732 89.933 8336 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.61 % Favored : 98.35 % Rotamer: Outliers : 0.51 % Allowed : 22.27 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.15), residues: 2426 helix: -0.48 (0.11), residues: 1605 sheet: 0.58 (0.49), residues: 121 loop : -1.02 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.055 0.001 ARG F 137 TYR 0.012 0.001 TYR O 127 PHE 0.016 0.001 PHE a 94 TRP 0.011 0.001 TRP I 108 HIS 0.005 0.002 HIS F 48 Details of bonding type rmsd covalent geometry : bond 0.00664 (19939) covalent geometry : angle 0.71779 (27174) SS BOND : bond 0.12715 ( 5) SS BOND : angle 7.43768 ( 10) hydrogen bonds : bond 0.31044 ( 1241) hydrogen bonds : angle 7.57967 ( 3657) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 645 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 THR cc_start: 0.8837 (p) cc_final: 0.8392 (p) REVERT: B 148 GLN cc_start: 0.8319 (mp10) cc_final: 0.8060 (mp10) REVERT: B 151 MET cc_start: 0.7758 (mmm) cc_final: 0.7260 (tpt) REVERT: B 157 ASP cc_start: 0.8504 (t0) cc_final: 0.8254 (t0) REVERT: B 158 CYS cc_start: 0.7494 (m) cc_final: 0.6983 (p) REVERT: C 53 LYS cc_start: 0.8897 (tttm) cc_final: 0.8417 (tmtt) REVERT: F 13 ASP cc_start: 0.8679 (t70) cc_final: 0.8407 (t0) REVERT: G 170 ASP cc_start: 0.8622 (m-30) cc_final: 0.8401 (m-30) REVERT: I 1 MET cc_start: 0.8466 (mmt) cc_final: 0.8176 (mmt) REVERT: I 69 PRO cc_start: 0.9119 (Cg_exo) cc_final: 0.8296 (Cg_endo) REVERT: I 102 THR cc_start: 0.8910 (p) cc_final: 0.8427 (p) REVERT: I 121 ASN cc_start: 0.8611 (t0) cc_final: 0.8341 (t0) REVERT: J 54 ASP cc_start: 0.7966 (t70) cc_final: 0.7537 (t0) REVERT: J 101 ASP cc_start: 0.8321 (t0) cc_final: 0.8003 (t0) REVERT: J 151 MET cc_start: 0.7173 (tpt) cc_final: 0.6886 (mmt) REVERT: M 63 ASN cc_start: 0.8677 (t0) cc_final: 0.8460 (t0) REVERT: M 111 ASN cc_start: 0.9012 (t0) cc_final: 0.8744 (t0) REVERT: a 35 PHE cc_start: 0.6200 (m-80) cc_final: 0.5919 (m-10) REVERT: a 69 TYR cc_start: 0.7768 (p90) cc_final: 0.7507 (p90) REVERT: a 86 PHE cc_start: 0.6185 (m-80) cc_final: 0.5493 (m-80) REVERT: a 123 ASP cc_start: -0.0181 (m-30) cc_final: -0.0553 (t0) REVERT: b 74 HIS cc_start: 0.8288 (m90) cc_final: 0.8084 (m-70) REVERT: b 189 LEU cc_start: 0.7584 (pt) cc_final: 0.7236 (tp) outliers start: 10 outliers final: 5 residues processed: 649 average time/residue: 0.1729 time to fit residues: 162.6988 Evaluate side-chains 493 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 488 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 50 CYS Chi-restraints excluded: chain I residue 137 ARG Chi-restraints excluded: chain I residue 139 CYS Chi-restraints excluded: chain O residue 144 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.0070 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 10.0000 overall best weight: 1.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 72 ASN ** J 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 6 GLN a 24 ASN a 73 HIS b 38 GLN b 118 ASN b 153 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.102398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.072188 restraints weight = 45268.307| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.06 r_work: 0.2925 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19944 Z= 0.166 Angle : 0.650 10.669 27184 Z= 0.324 Chirality : 0.038 0.170 2997 Planarity : 0.004 0.064 3471 Dihedral : 14.127 87.878 4375 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.07 % Favored : 98.89 % Rotamer: Outliers : 4.63 % Allowed : 21.09 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.16), residues: 2426 helix: 1.72 (0.12), residues: 1641 sheet: 0.87 (0.53), residues: 91 loop : -0.89 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 142 TYR 0.013 0.001 TYR B 168 PHE 0.014 0.001 PHE a 94 TRP 0.013 0.001 TRP a 34 HIS 0.008 0.002 HIS I 48 Details of bonding type rmsd covalent geometry : bond 0.00346 (19939) covalent geometry : angle 0.64929 (27174) SS BOND : bond 0.00533 ( 5) SS BOND : angle 1.08035 ( 10) hydrogen bonds : bond 0.06819 ( 1241) hydrogen bonds : angle 4.40835 ( 3657) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 581 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 THR cc_start: 0.8569 (p) cc_final: 0.7654 (p) REVERT: A 106 ASP cc_start: 0.8949 (m-30) cc_final: 0.8330 (m-30) REVERT: A 115 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8454 (mp0) REVERT: A 144 MET cc_start: 0.8461 (ptp) cc_final: 0.8162 (ptp) REVERT: B 101 ASP cc_start: 0.8373 (t0) cc_final: 0.8072 (t0) REVERT: B 106 GLU cc_start: 0.9162 (tt0) cc_final: 0.8647 (tm-30) REVERT: B 107 ASP cc_start: 0.8904 (OUTLIER) cc_final: 0.8648 (t0) REVERT: B 148 GLN cc_start: 0.8885 (mp10) cc_final: 0.8591 (mp10) REVERT: B 151 MET cc_start: 0.8215 (mmm) cc_final: 0.7248 (tpt) REVERT: B 157 ASP cc_start: 0.8864 (t0) cc_final: 0.8647 (t0) REVERT: B 158 CYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7488 (p) REVERT: C 53 LYS cc_start: 0.8805 (tttm) cc_final: 0.8386 (tmtt) REVERT: C 57 ASP cc_start: 0.8891 (m-30) cc_final: 0.8526 (m-30) REVERT: C 71 GLU cc_start: 0.8590 (mp0) cc_final: 0.7827 (mp0) REVERT: C 77 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7564 (tm-30) REVERT: C 114 ARG cc_start: 0.8970 (ttp-170) cc_final: 0.8716 (ptp-110) REVERT: C 115 GLU cc_start: 0.9029 (mp0) cc_final: 0.8402 (mp0) REVERT: C 137 ARG cc_start: 0.8853 (ttt90) cc_final: 0.8649 (ttt90) REVERT: D 101 ASP cc_start: 0.8859 (t70) cc_final: 0.8132 (t0) REVERT: D 148 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8700 (pm20) REVERT: F 144 MET cc_start: 0.9067 (pmm) cc_final: 0.8695 (pmm) REVERT: I 1 MET cc_start: 0.8276 (mmt) cc_final: 0.7781 (mmt) REVERT: I 54 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8123 (mt-10) REVERT: I 71 GLU cc_start: 0.8242 (mp0) cc_final: 0.8040 (mp0) REVERT: I 102 THR cc_start: 0.8060 (p) cc_final: 0.7742 (p) REVERT: I 110 ILE cc_start: 0.9628 (OUTLIER) cc_final: 0.9390 (mm) REVERT: I 115 GLU cc_start: 0.8668 (mp0) cc_final: 0.8385 (mp0) REVERT: J 39 ASP cc_start: 0.8889 (t0) cc_final: 0.8599 (m-30) REVERT: J 111 ASN cc_start: 0.9036 (t0) cc_final: 0.8823 (t0) REVERT: J 151 MET cc_start: 0.6909 (tpt) cc_final: 0.6698 (mmt) REVERT: L 106 ASP cc_start: 0.8755 (m-30) cc_final: 0.8456 (m-30) REVERT: M 63 ASN cc_start: 0.8223 (t0) cc_final: 0.7693 (t0) REVERT: M 111 ASN cc_start: 0.9303 (t0) cc_final: 0.8932 (t0) REVERT: O 1 MET cc_start: 0.8196 (mmm) cc_final: 0.7568 (tpp) REVERT: O 147 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8006 (mp10) REVERT: Q 61 CYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8011 (p) REVERT: a 33 GLN cc_start: 0.7890 (mt0) cc_final: 0.7315 (mm110) REVERT: a 45 ASN cc_start: 0.8285 (t0) cc_final: 0.8078 (t0) REVERT: a 64 ASP cc_start: 0.7615 (t0) cc_final: 0.7303 (t0) REVERT: a 69 TYR cc_start: 0.8688 (p90) cc_final: 0.8200 (p90) REVERT: a 86 PHE cc_start: 0.7044 (m-80) cc_final: 0.6141 (m-80) REVERT: a 94 PHE cc_start: 0.7949 (m-80) cc_final: 0.7317 (m-80) REVERT: a 123 ASP cc_start: 0.0695 (m-30) cc_final: 0.0355 (t0) REVERT: b 24 CYS cc_start: 0.2898 (p) cc_final: 0.1856 (t) REVERT: b 30 HIS cc_start: 0.7004 (m90) cc_final: 0.6640 (m-70) REVERT: b 50 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.7699 (t80) REVERT: b 53 LYS cc_start: 0.7852 (mmmt) cc_final: 0.7624 (mmtt) REVERT: b 74 HIS cc_start: 0.8892 (m90) cc_final: 0.8576 (m-70) REVERT: b 189 LEU cc_start: 0.7579 (pt) cc_final: 0.6772 (tp) outliers start: 90 outliers final: 40 residues processed: 633 average time/residue: 0.1629 time to fit residues: 153.3102 Evaluate side-chains 546 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 498 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 148 GLN Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain I residue 110 ILE Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 128 ILE Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 31 ILE Chi-restraints excluded: chain O residue 106 ASP Chi-restraints excluded: chain O residue 109 CYS Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 147 GLN Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain Q residue 61 CYS Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 158 CYS Chi-restraints excluded: chain Q residue 163 SER Chi-restraints excluded: chain Q residue 170 ASP Chi-restraints excluded: chain a residue 24 ASN Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain b residue 50 TYR Chi-restraints excluded: chain b residue 118 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 116 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 160 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 209 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 7 optimal weight: 0.0020 chunk 171 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN D 72 ASN F 28 GLN ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 24 ASN ** b 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 153 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.102544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.071910 restraints weight = 45479.126| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.17 r_work: 0.2911 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19944 Z= 0.128 Angle : 0.557 8.426 27184 Z= 0.281 Chirality : 0.037 0.148 2997 Planarity : 0.004 0.055 3471 Dihedral : 13.136 88.341 4363 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 0.78 % Favored : 99.18 % Rotamer: Outliers : 3.19 % Allowed : 23.25 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.17), residues: 2426 helix: 2.29 (0.12), residues: 1659 sheet: 0.70 (0.50), residues: 100 loop : -0.75 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 114 TYR 0.019 0.001 TYR O 127 PHE 0.037 0.001 PHE b 48 TRP 0.024 0.002 TRP b 35 HIS 0.006 0.001 HIS b 153 Details of bonding type rmsd covalent geometry : bond 0.00270 (19939) covalent geometry : angle 0.55634 (27174) SS BOND : bond 0.00953 ( 5) SS BOND : angle 0.96436 ( 10) hydrogen bonds : bond 0.04897 ( 1241) hydrogen bonds : angle 3.91084 ( 3657) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 530 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 THR cc_start: 0.8311 (p) cc_final: 0.7390 (p) REVERT: A 106 ASP cc_start: 0.8967 (m-30) cc_final: 0.8368 (m-30) REVERT: A 115 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8466 (mp0) REVERT: A 144 MET cc_start: 0.8433 (ptp) cc_final: 0.8083 (ptp) REVERT: B 15 LYS cc_start: 0.9176 (mtmm) cc_final: 0.8678 (mppt) REVERT: B 148 GLN cc_start: 0.8777 (mp10) cc_final: 0.8402 (mp10) REVERT: B 151 MET cc_start: 0.8282 (mmm) cc_final: 0.7211 (tpt) REVERT: B 158 CYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7185 (p) REVERT: B 164 GLU cc_start: 0.8848 (tp30) cc_final: 0.8520 (tp30) REVERT: C 53 LYS cc_start: 0.8779 (tttm) cc_final: 0.8318 (tmtt) REVERT: C 57 ASP cc_start: 0.8872 (m-30) cc_final: 0.8429 (m-30) REVERT: C 71 GLU cc_start: 0.8648 (mp0) cc_final: 0.7856 (mp0) REVERT: C 114 ARG cc_start: 0.8996 (ttp-170) cc_final: 0.8629 (ptm-80) REVERT: C 115 GLU cc_start: 0.9084 (mp0) cc_final: 0.8473 (mp0) REVERT: C 137 ARG cc_start: 0.8807 (ttt90) cc_final: 0.8571 (ttt90) REVERT: D 3 ASP cc_start: 0.8232 (p0) cc_final: 0.7914 (p0) REVERT: D 148 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8897 (pm20) REVERT: F 62 LYS cc_start: 0.9305 (tppt) cc_final: 0.8948 (tptm) REVERT: F 144 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8641 (pmm) REVERT: I 1 MET cc_start: 0.8085 (mmt) cc_final: 0.7734 (mmt) REVERT: I 53 LYS cc_start: 0.8314 (mmmm) cc_final: 0.8097 (tppt) REVERT: I 102 THR cc_start: 0.7771 (p) cc_final: 0.7420 (p) REVERT: I 115 GLU cc_start: 0.8663 (mp0) cc_final: 0.8433 (mp0) REVERT: J 108 ARG cc_start: 0.8674 (mmm-85) cc_final: 0.8452 (mmm-85) REVERT: J 111 ASN cc_start: 0.9002 (t0) cc_final: 0.8705 (t0) REVERT: J 150 LYS cc_start: 0.9100 (mmmm) cc_final: 0.8641 (mmmt) REVERT: J 164 GLU cc_start: 0.8839 (tt0) cc_final: 0.8567 (tp30) REVERT: L 106 ASP cc_start: 0.8621 (m-30) cc_final: 0.8161 (m-30) REVERT: L 107 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8348 (mt-10) REVERT: L 136 ASP cc_start: 0.8749 (m-30) cc_final: 0.8536 (t0) REVERT: O 147 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7995 (mp10) REVERT: O 151 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8494 (mm-30) REVERT: a 33 GLN cc_start: 0.7825 (mt0) cc_final: 0.7436 (mm-40) REVERT: a 64 ASP cc_start: 0.7826 (t0) cc_final: 0.7488 (t0) REVERT: a 69 TYR cc_start: 0.8721 (p90) cc_final: 0.8261 (p90) REVERT: a 86 PHE cc_start: 0.7274 (m-80) cc_final: 0.6174 (m-80) REVERT: a 123 ASP cc_start: 0.0864 (m-30) cc_final: 0.0461 (t0) REVERT: b 30 HIS cc_start: 0.6677 (m-70) cc_final: 0.6284 (m170) REVERT: b 50 TYR cc_start: 0.8124 (t80) cc_final: 0.7438 (t80) REVERT: b 54 GLN cc_start: 0.8289 (pp30) cc_final: 0.7685 (pm20) REVERT: b 74 HIS cc_start: 0.8824 (m90) cc_final: 0.8528 (m-70) REVERT: b 118 ASN cc_start: 0.2237 (OUTLIER) cc_final: 0.1943 (p0) REVERT: b 189 LEU cc_start: 0.7600 (pt) cc_final: 0.6761 (tp) outliers start: 62 outliers final: 37 residues processed: 562 average time/residue: 0.1520 time to fit residues: 126.6363 Evaluate side-chains 548 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 505 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 148 GLN Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 125 SER Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 59 CYS Chi-restraints excluded: chain O residue 109 CYS Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 147 GLN Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain Q residue 44 ILE Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 142 ILE Chi-restraints excluded: chain a residue 24 ASN Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 118 ASN Chi-restraints excluded: chain b residue 119 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 43 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 208 optimal weight: 20.0000 chunk 116 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 189 optimal weight: 6.9990 chunk 235 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 238 optimal weight: 2.9990 chunk 190 optimal weight: 0.9980 chunk 230 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 72 ASN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 121 ASN a 24 ASN b 118 ASN ** b 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.095728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.066017 restraints weight = 46036.145| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.93 r_work: 0.2796 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 19944 Z= 0.282 Angle : 0.714 11.249 27184 Z= 0.351 Chirality : 0.042 0.159 2997 Planarity : 0.004 0.059 3471 Dihedral : 12.524 89.840 4363 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.40 % Favored : 98.56 % Rotamer: Outliers : 4.99 % Allowed : 23.41 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.17), residues: 2426 helix: 2.19 (0.12), residues: 1659 sheet: 0.84 (0.47), residues: 113 loop : -0.82 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 118 TYR 0.023 0.002 TYR J 92 PHE 0.025 0.002 PHE b 48 TRP 0.014 0.001 TRP a 34 HIS 0.009 0.002 HIS I 48 Details of bonding type rmsd covalent geometry : bond 0.00636 (19939) covalent geometry : angle 0.71439 (27174) SS BOND : bond 0.00374 ( 5) SS BOND : angle 0.91369 ( 10) hydrogen bonds : bond 0.06748 ( 1241) hydrogen bonds : angle 4.34425 ( 3657) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 513 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.8852 (ttm110) cc_final: 0.8538 (mtm-85) REVERT: A 115 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8543 (mp0) REVERT: A 144 MET cc_start: 0.8528 (ptp) cc_final: 0.8161 (ptp) REVERT: B 29 THR cc_start: 0.9228 (OUTLIER) cc_final: 0.8992 (p) REVERT: B 101 ASP cc_start: 0.8584 (t0) cc_final: 0.8091 (t0) REVERT: B 148 GLN cc_start: 0.8828 (mp10) cc_final: 0.8395 (mp10) REVERT: B 170 ASP cc_start: 0.9115 (t0) cc_final: 0.8912 (t0) REVERT: C 53 LYS cc_start: 0.8838 (tttm) cc_final: 0.8356 (tmtt) REVERT: C 57 ASP cc_start: 0.8926 (m-30) cc_final: 0.8482 (m-30) REVERT: C 62 LYS cc_start: 0.9528 (tptp) cc_final: 0.9224 (tptt) REVERT: C 71 GLU cc_start: 0.8836 (mp0) cc_final: 0.8298 (mp0) REVERT: C 115 GLU cc_start: 0.9037 (mp0) cc_final: 0.8497 (mp0) REVERT: D 101 ASP cc_start: 0.8975 (t70) cc_final: 0.8161 (t0) REVERT: F 62 LYS cc_start: 0.9371 (tppt) cc_final: 0.9042 (tptm) REVERT: F 74 ASP cc_start: 0.8402 (p0) cc_final: 0.8161 (p0) REVERT: F 151 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8553 (mm-30) REVERT: G 77 ARG cc_start: 0.9328 (ttp80) cc_final: 0.9122 (ttp80) REVERT: G 148 GLN cc_start: 0.8715 (mp10) cc_final: 0.8445 (mp10) REVERT: I 1 MET cc_start: 0.8345 (mmt) cc_final: 0.7945 (mmt) REVERT: I 32 GLN cc_start: 0.8879 (tm-30) cc_final: 0.8641 (tm-30) REVERT: I 42 GLU cc_start: 0.9119 (tp30) cc_final: 0.8899 (tm-30) REVERT: I 54 GLU cc_start: 0.8484 (mt-10) cc_final: 0.7894 (mt-10) REVERT: I 102 THR cc_start: 0.8316 (p) cc_final: 0.7934 (p) REVERT: I 114 ARG cc_start: 0.8736 (mtp-110) cc_final: 0.8375 (mtp85) REVERT: I 115 GLU cc_start: 0.8737 (mp0) cc_final: 0.8488 (mp0) REVERT: I 137 ARG cc_start: 0.8934 (mmp80) cc_final: 0.8693 (tpp80) REVERT: I 144 MET cc_start: 0.7647 (ttm) cc_final: 0.7195 (ttm) REVERT: J 54 ASP cc_start: 0.8864 (t70) cc_final: 0.8451 (t0) REVERT: J 101 ASP cc_start: 0.8636 (t0) cc_final: 0.8112 (t0) REVERT: J 107 ASP cc_start: 0.8373 (m-30) cc_final: 0.8038 (m-30) REVERT: J 111 ASN cc_start: 0.9095 (t0) cc_final: 0.8768 (t0) REVERT: J 150 LYS cc_start: 0.9234 (mmmm) cc_final: 0.8765 (mmmt) REVERT: L 39 GLU cc_start: 0.8811 (tp30) cc_final: 0.8514 (tp30) REVERT: L 89 TYR cc_start: 0.9407 (m-80) cc_final: 0.9098 (m-80) REVERT: L 106 ASP cc_start: 0.8926 (m-30) cc_final: 0.8668 (m-30) REVERT: L 121 ASN cc_start: 0.9301 (t0) cc_final: 0.9075 (t0) REVERT: O 71 GLU cc_start: 0.8529 (mp0) cc_final: 0.8261 (mp0) REVERT: O 81 LYS cc_start: 0.9110 (mttt) cc_final: 0.8834 (mttp) REVERT: O 107 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8590 (mt-10) REVERT: O 110 ILE cc_start: 0.9548 (mm) cc_final: 0.9326 (mm) REVERT: O 137 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.8512 (ttm-80) REVERT: Q 61 CYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8238 (p) REVERT: a 33 GLN cc_start: 0.7931 (mt0) cc_final: 0.7058 (mm110) REVERT: a 64 ASP cc_start: 0.7789 (t0) cc_final: 0.7415 (t0) REVERT: a 69 TYR cc_start: 0.8728 (p90) cc_final: 0.8280 (p90) REVERT: a 71 THR cc_start: 0.7433 (OUTLIER) cc_final: 0.6966 (t) REVERT: a 94 PHE cc_start: 0.8185 (m-80) cc_final: 0.7914 (m-80) REVERT: a 95 ASN cc_start: 0.5824 (t0) cc_final: 0.5501 (t0) REVERT: a 123 ASP cc_start: 0.0934 (m-30) cc_final: 0.0642 (t0) REVERT: b 50 TYR cc_start: 0.8189 (t80) cc_final: 0.7444 (t80) REVERT: b 54 GLN cc_start: 0.8527 (pp30) cc_final: 0.7953 (pm20) REVERT: b 74 HIS cc_start: 0.8797 (m90) cc_final: 0.8566 (m-70) REVERT: b 189 LEU cc_start: 0.7731 (pt) cc_final: 0.6815 (tp) outliers start: 97 outliers final: 61 residues processed: 570 average time/residue: 0.1516 time to fit residues: 129.5429 Evaluate side-chains 529 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 463 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 61 CYS Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 59 CYS Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 125 SER Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 61 CYS Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 158 CYS Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 31 ILE Chi-restraints excluded: chain O residue 109 CYS Chi-restraints excluded: chain O residue 137 ARG Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 44 ILE Chi-restraints excluded: chain Q residue 61 CYS Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 170 ASP Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 71 THR Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain b residue 52 ASN Chi-restraints excluded: chain b residue 57 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 146 optimal weight: 0.9980 chunk 47 optimal weight: 0.2980 chunk 166 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 206 optimal weight: 30.0000 chunk 225 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 72 ASN O 68 ASN O 121 ASN ** b 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 212 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.098436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.067777 restraints weight = 45462.778| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.31 r_work: 0.2891 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19944 Z= 0.129 Angle : 0.564 10.753 27184 Z= 0.285 Chirality : 0.037 0.165 2997 Planarity : 0.004 0.053 3471 Dihedral : 11.998 89.574 4363 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 0.99 % Favored : 98.97 % Rotamer: Outliers : 3.60 % Allowed : 24.95 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.55 (0.17), residues: 2426 helix: 2.63 (0.13), residues: 1659 sheet: 0.67 (0.46), residues: 118 loop : -0.69 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 118 TYR 0.018 0.001 TYR B 168 PHE 0.019 0.001 PHE b 48 TRP 0.037 0.001 TRP a 34 HIS 0.007 0.001 HIS b 153 Details of bonding type rmsd covalent geometry : bond 0.00283 (19939) covalent geometry : angle 0.56417 (27174) SS BOND : bond 0.00275 ( 5) SS BOND : angle 0.77886 ( 10) hydrogen bonds : bond 0.04590 ( 1241) hydrogen bonds : angle 3.76685 ( 3657) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 519 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.8847 (ttm110) cc_final: 0.8539 (ttp80) REVERT: A 115 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8544 (mp0) REVERT: A 144 MET cc_start: 0.8485 (ptp) cc_final: 0.8120 (ptp) REVERT: B 101 ASP cc_start: 0.8540 (t0) cc_final: 0.8006 (t0) REVERT: B 106 GLU cc_start: 0.9187 (tt0) cc_final: 0.8690 (tm-30) REVERT: B 148 GLN cc_start: 0.8769 (mp10) cc_final: 0.8388 (mp10) REVERT: B 170 ASP cc_start: 0.9133 (t0) cc_final: 0.8898 (t0) REVERT: C 39 GLU cc_start: 0.8903 (tp30) cc_final: 0.8635 (tp30) REVERT: C 42 GLU cc_start: 0.9050 (tm-30) cc_final: 0.8681 (tm-30) REVERT: C 53 LYS cc_start: 0.8821 (tttm) cc_final: 0.8251 (tmtt) REVERT: C 57 ASP cc_start: 0.8904 (m-30) cc_final: 0.8396 (m-30) REVERT: C 62 LYS cc_start: 0.9412 (tptp) cc_final: 0.9206 (tptt) REVERT: C 71 GLU cc_start: 0.8793 (mp0) cc_final: 0.8291 (mp0) REVERT: C 77 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7836 (tm-30) REVERT: C 107 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8632 (mm-30) REVERT: C 115 GLU cc_start: 0.9021 (mp0) cc_final: 0.8592 (mp0) REVERT: D 108 ARG cc_start: 0.9147 (mtt180) cc_final: 0.8670 (mtp85) REVERT: F 2 LYS cc_start: 0.9109 (tttp) cc_final: 0.8882 (tptp) REVERT: F 74 ASP cc_start: 0.8373 (p0) cc_final: 0.8152 (p0) REVERT: F 114 ARG cc_start: 0.8917 (ttm-80) cc_final: 0.8556 (mtt-85) REVERT: G 1 MET cc_start: 0.8196 (tmm) cc_final: 0.7839 (tmm) REVERT: G 25 GLN cc_start: 0.8799 (mm-40) cc_final: 0.8451 (mm-40) REVERT: G 77 ARG cc_start: 0.9174 (ttp80) cc_final: 0.8926 (ttp80) REVERT: G 148 GLN cc_start: 0.8753 (mp10) cc_final: 0.8430 (mp10) REVERT: I 1 MET cc_start: 0.8235 (mmt) cc_final: 0.7856 (mmt) REVERT: I 54 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7789 (mt-10) REVERT: I 102 THR cc_start: 0.8054 (p) cc_final: 0.7690 (p) REVERT: I 114 ARG cc_start: 0.8655 (mtp-110) cc_final: 0.8386 (mtp85) REVERT: I 115 GLU cc_start: 0.8802 (mp0) cc_final: 0.8523 (mp0) REVERT: I 121 ASN cc_start: 0.9046 (t0) cc_final: 0.8764 (t0) REVERT: J 54 ASP cc_start: 0.8807 (t70) cc_final: 0.8359 (t0) REVERT: J 101 ASP cc_start: 0.8331 (t0) cc_final: 0.7905 (t0) REVERT: J 107 ASP cc_start: 0.8445 (m-30) cc_final: 0.8171 (m-30) REVERT: J 150 LYS cc_start: 0.9190 (mmmm) cc_final: 0.8759 (mmmt) REVERT: L 106 ASP cc_start: 0.8792 (m-30) cc_final: 0.8380 (m-30) REVERT: M 95 TYR cc_start: 0.8826 (m-10) cc_final: 0.8561 (m-10) REVERT: O 71 GLU cc_start: 0.8510 (mp0) cc_final: 0.8244 (mp0) REVERT: O 107 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8342 (tm-30) REVERT: O 114 ARG cc_start: 0.8685 (mmm-85) cc_final: 0.8262 (mmm-85) REVERT: Q 25 GLN cc_start: 0.9167 (tp-100) cc_final: 0.8873 (tm-30) REVERT: Q 61 CYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8181 (p) REVERT: a 22 ARG cc_start: 0.8780 (ttt180) cc_final: 0.8426 (mmm160) REVERT: a 24 ASN cc_start: 0.8187 (OUTLIER) cc_final: 0.7888 (m-40) REVERT: a 33 GLN cc_start: 0.7953 (mt0) cc_final: 0.6997 (mm110) REVERT: a 64 ASP cc_start: 0.7744 (t0) cc_final: 0.7359 (t0) REVERT: a 69 TYR cc_start: 0.8539 (p90) cc_final: 0.8331 (p90) REVERT: a 71 THR cc_start: 0.7606 (OUTLIER) cc_final: 0.6653 (t) REVERT: a 94 PHE cc_start: 0.8186 (m-80) cc_final: 0.7962 (m-80) REVERT: a 123 ASP cc_start: 0.1049 (m-30) cc_final: 0.0715 (t0) REVERT: b 6 PHE cc_start: 0.7624 (p90) cc_final: 0.7390 (p90) REVERT: b 19 GLU cc_start: 0.7569 (tp30) cc_final: 0.5639 (tp30) REVERT: b 50 TYR cc_start: 0.8175 (t80) cc_final: 0.7404 (t80) REVERT: b 54 GLN cc_start: 0.8500 (pp30) cc_final: 0.7953 (pm20) REVERT: b 74 HIS cc_start: 0.8819 (m90) cc_final: 0.8549 (m-70) REVERT: b 189 LEU cc_start: 0.7789 (pt) cc_final: 0.6828 (tp) outliers start: 70 outliers final: 44 residues processed: 563 average time/residue: 0.1560 time to fit residues: 130.8251 Evaluate side-chains 529 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 481 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 59 CYS Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 61 CYS Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 158 CYS Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 42 GLU Chi-restraints excluded: chain O residue 109 CYS Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain Q residue 44 ILE Chi-restraints excluded: chain Q residue 61 CYS Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 134 MET Chi-restraints excluded: chain Q residue 142 ILE Chi-restraints excluded: chain Q residue 163 SER Chi-restraints excluded: chain a residue 23 CYS Chi-restraints excluded: chain a residue 24 ASN Chi-restraints excluded: chain a residue 63 PHE Chi-restraints excluded: chain a residue 71 THR Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain b residue 119 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 155 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 25 optimal weight: 0.0970 chunk 80 optimal weight: 0.9990 chunk 172 optimal weight: 0.7980 chunk 204 optimal weight: 8.9990 chunk 179 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 192 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 72 ASN L 48 HIS ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 121 ASN a 95 ASN b 76 ASN b 118 ASN ** b 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 212 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.099638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.069224 restraints weight = 45237.186| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.28 r_work: 0.2859 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19944 Z= 0.118 Angle : 0.556 9.328 27184 Z= 0.280 Chirality : 0.036 0.166 2997 Planarity : 0.004 0.051 3471 Dihedral : 11.654 89.487 4363 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.15 % Favored : 98.80 % Rotamer: Outliers : 3.55 % Allowed : 25.15 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.78 (0.17), residues: 2426 helix: 2.80 (0.13), residues: 1659 sheet: 0.86 (0.46), residues: 113 loop : -0.62 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 7 TYR 0.012 0.001 TYR Q 168 PHE 0.016 0.001 PHE b 48 TRP 0.037 0.001 TRP a 34 HIS 0.006 0.001 HIS b 153 Details of bonding type rmsd covalent geometry : bond 0.00258 (19939) covalent geometry : angle 0.55638 (27174) SS BOND : bond 0.00413 ( 5) SS BOND : angle 0.55976 ( 10) hydrogen bonds : bond 0.04104 ( 1241) hydrogen bonds : angle 3.58521 ( 3657) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 504 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.8805 (ttm110) cc_final: 0.8175 (ttp80) REVERT: A 115 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8560 (mp0) REVERT: A 144 MET cc_start: 0.8404 (ptp) cc_final: 0.7986 (ptp) REVERT: B 15 LYS cc_start: 0.9219 (mtmm) cc_final: 0.8779 (mppt) REVERT: B 101 ASP cc_start: 0.8555 (t0) cc_final: 0.7976 (t0) REVERT: B 107 ASP cc_start: 0.8972 (t0) cc_final: 0.8693 (m-30) REVERT: B 148 GLN cc_start: 0.8739 (mp10) cc_final: 0.8358 (mp10) REVERT: B 164 GLU cc_start: 0.8655 (tp30) cc_final: 0.8313 (tp30) REVERT: B 170 ASP cc_start: 0.9156 (t0) cc_final: 0.8909 (t0) REVERT: C 42 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8624 (tm-30) REVERT: C 53 LYS cc_start: 0.8738 (tttm) cc_final: 0.8161 (tmtt) REVERT: C 57 ASP cc_start: 0.8852 (m-30) cc_final: 0.8309 (m-30) REVERT: C 62 LYS cc_start: 0.9363 (tptp) cc_final: 0.9124 (tptt) REVERT: C 71 GLU cc_start: 0.8805 (mp0) cc_final: 0.8339 (mp0) REVERT: C 107 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8640 (mm-30) REVERT: C 114 ARG cc_start: 0.8772 (ptp-110) cc_final: 0.8460 (mtp-110) REVERT: D 3 ASP cc_start: 0.8179 (p0) cc_final: 0.7878 (p0) REVERT: D 108 ARG cc_start: 0.9099 (mtt180) cc_final: 0.8689 (mtp85) REVERT: F 2 LYS cc_start: 0.9043 (tttp) cc_final: 0.8829 (tptp) REVERT: F 62 LYS cc_start: 0.9271 (tppt) cc_final: 0.8731 (tptm) REVERT: F 71 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8156 (mm-30) REVERT: F 74 ASP cc_start: 0.8223 (p0) cc_final: 0.7966 (p0) REVERT: F 114 ARG cc_start: 0.8867 (ttm-80) cc_final: 0.8513 (mtt-85) REVERT: F 151 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8669 (mm-30) REVERT: G 25 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8423 (mm-40) REVERT: G 77 ARG cc_start: 0.9115 (ttp80) cc_final: 0.8827 (ttp80) REVERT: G 148 GLN cc_start: 0.8752 (mp10) cc_final: 0.8388 (mp10) REVERT: I 1 MET cc_start: 0.8055 (mmt) cc_final: 0.7668 (mmt) REVERT: I 54 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7726 (mt-10) REVERT: I 102 THR cc_start: 0.7823 (p) cc_final: 0.7466 (p) REVERT: I 114 ARG cc_start: 0.8659 (mtp-110) cc_final: 0.8408 (mtp85) REVERT: I 115 GLU cc_start: 0.8815 (mp0) cc_final: 0.8487 (mp0) REVERT: I 121 ASN cc_start: 0.8998 (t0) cc_final: 0.8704 (t0) REVERT: J 54 ASP cc_start: 0.8780 (t70) cc_final: 0.8379 (t0) REVERT: J 101 ASP cc_start: 0.8159 (t0) cc_final: 0.7715 (t0) REVERT: J 107 ASP cc_start: 0.8387 (m-30) cc_final: 0.8186 (m-30) REVERT: J 150 LYS cc_start: 0.9240 (mmmm) cc_final: 0.8844 (mmmt) REVERT: J 164 GLU cc_start: 0.9005 (tp30) cc_final: 0.8631 (tp30) REVERT: L 106 ASP cc_start: 0.8673 (m-30) cc_final: 0.8249 (m-30) REVERT: M 25 GLN cc_start: 0.8777 (tp40) cc_final: 0.8542 (tp40) REVERT: M 95 TYR cc_start: 0.8658 (m-10) cc_final: 0.8444 (m-10) REVERT: M 129 ARG cc_start: 0.8801 (tpt170) cc_final: 0.8428 (tpt170) REVERT: O 71 GLU cc_start: 0.8520 (mp0) cc_final: 0.8242 (mp0) REVERT: O 107 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8229 (tm-30) REVERT: O 114 ARG cc_start: 0.8644 (mmm-85) cc_final: 0.8382 (mmm-85) REVERT: Q 23 ASP cc_start: 0.9181 (OUTLIER) cc_final: 0.8978 (t0) REVERT: Q 25 GLN cc_start: 0.9184 (tp-100) cc_final: 0.8911 (tm-30) REVERT: a 22 ARG cc_start: 0.8786 (ttt180) cc_final: 0.8411 (mtp85) REVERT: a 33 GLN cc_start: 0.7768 (mt0) cc_final: 0.6817 (mm-40) REVERT: a 46 LEU cc_start: 0.8651 (pp) cc_final: 0.8117 (pp) REVERT: a 47 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.7266 (m-10) REVERT: a 64 ASP cc_start: 0.7682 (t0) cc_final: 0.7286 (t0) REVERT: a 71 THR cc_start: 0.7517 (OUTLIER) cc_final: 0.6924 (t) REVERT: a 123 ASP cc_start: 0.1341 (m-30) cc_final: 0.0980 (t0) REVERT: b 6 PHE cc_start: 0.7672 (p90) cc_final: 0.7457 (p90) REVERT: b 19 GLU cc_start: 0.7538 (tp30) cc_final: 0.5653 (tp30) REVERT: b 37 LYS cc_start: 0.7211 (tptt) cc_final: 0.6982 (tttp) REVERT: b 50 TYR cc_start: 0.8123 (t80) cc_final: 0.7720 (t80) REVERT: b 54 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8098 (pm20) REVERT: b 76 ASN cc_start: 0.6436 (m-40) cc_final: 0.5795 (m110) REVERT: b 189 LEU cc_start: 0.7667 (pt) cc_final: 0.6716 (tp) outliers start: 69 outliers final: 47 residues processed: 546 average time/residue: 0.1625 time to fit residues: 132.5393 Evaluate side-chains 532 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 480 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 61 CYS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 59 CYS Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 125 SER Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 61 CYS Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 158 CYS Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 109 CYS Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain Q residue 23 ASP Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain Q residue 44 ILE Chi-restraints excluded: chain Q residue 50 CYS Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 134 MET Chi-restraints excluded: chain Q residue 142 ILE Chi-restraints excluded: chain Q residue 163 SER Chi-restraints excluded: chain a residue 23 CYS Chi-restraints excluded: chain a residue 47 PHE Chi-restraints excluded: chain a residue 63 PHE Chi-restraints excluded: chain a residue 71 THR Chi-restraints excluded: chain b residue 54 GLN Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 119 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 28 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 205 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 chunk 106 optimal weight: 0.0570 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN D 72 ASN O 68 ASN O 121 ASN b 118 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.098924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.068305 restraints weight = 45554.521| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.19 r_work: 0.2844 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19944 Z= 0.128 Angle : 0.558 9.109 27184 Z= 0.283 Chirality : 0.037 0.161 2997 Planarity : 0.004 0.050 3471 Dihedral : 11.537 88.467 4363 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.40 % Favored : 98.56 % Rotamer: Outliers : 3.70 % Allowed : 25.57 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.86 (0.17), residues: 2426 helix: 2.84 (0.13), residues: 1659 sheet: 0.93 (0.46), residues: 114 loop : -0.53 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 114 TYR 0.015 0.001 TYR B 168 PHE 0.016 0.001 PHE b 48 TRP 0.033 0.001 TRP a 34 HIS 0.006 0.001 HIS I 48 Details of bonding type rmsd covalent geometry : bond 0.00288 (19939) covalent geometry : angle 0.55831 (27174) SS BOND : bond 0.00331 ( 5) SS BOND : angle 0.75902 ( 10) hydrogen bonds : bond 0.04185 ( 1241) hydrogen bonds : angle 3.55042 ( 3657) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 482 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.8824 (ttm110) cc_final: 0.8037 (ttp80) REVERT: A 115 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8559 (mp0) REVERT: A 144 MET cc_start: 0.8428 (ptp) cc_final: 0.7994 (ptp) REVERT: B 15 LYS cc_start: 0.9208 (mtmm) cc_final: 0.8764 (mppt) REVERT: B 59 MET cc_start: 0.9139 (tmm) cc_final: 0.8707 (ttt) REVERT: B 101 ASP cc_start: 0.8609 (t0) cc_final: 0.8008 (t0) REVERT: B 107 ASP cc_start: 0.8975 (t0) cc_final: 0.8691 (m-30) REVERT: B 148 GLN cc_start: 0.8729 (mp10) cc_final: 0.8361 (mp10) REVERT: B 170 ASP cc_start: 0.9148 (t0) cc_final: 0.8883 (t0) REVERT: C 42 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8603 (tm-30) REVERT: C 53 LYS cc_start: 0.8747 (tttm) cc_final: 0.7970 (tmtt) REVERT: C 57 ASP cc_start: 0.8834 (m-30) cc_final: 0.7951 (m-30) REVERT: C 62 LYS cc_start: 0.9337 (tptp) cc_final: 0.9090 (tptt) REVERT: C 71 GLU cc_start: 0.8801 (mp0) cc_final: 0.8371 (mp0) REVERT: C 107 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8578 (mm-30) REVERT: C 114 ARG cc_start: 0.8775 (ptp-110) cc_final: 0.8436 (mtp85) REVERT: D 3 ASP cc_start: 0.8146 (p0) cc_final: 0.7854 (p0) REVERT: F 2 LYS cc_start: 0.9020 (tttp) cc_final: 0.8791 (tptp) REVERT: F 62 LYS cc_start: 0.9231 (tppt) cc_final: 0.8708 (tptm) REVERT: F 71 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8127 (mm-30) REVERT: F 74 ASP cc_start: 0.8216 (p0) cc_final: 0.7960 (p0) REVERT: F 114 ARG cc_start: 0.8911 (ttm-80) cc_final: 0.8538 (mtt-85) REVERT: F 151 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8644 (mm-30) REVERT: G 25 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8465 (mm-40) REVERT: G 77 ARG cc_start: 0.9136 (ttp80) cc_final: 0.8835 (ttp80) REVERT: G 148 GLN cc_start: 0.8808 (mp10) cc_final: 0.8437 (mp10) REVERT: I 1 MET cc_start: 0.8035 (mmt) cc_final: 0.7671 (mmt) REVERT: I 54 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7664 (mt-10) REVERT: I 102 THR cc_start: 0.7881 (p) cc_final: 0.7272 (p) REVERT: I 106 ASP cc_start: 0.8550 (m-30) cc_final: 0.8252 (m-30) REVERT: I 114 ARG cc_start: 0.8677 (mtp-110) cc_final: 0.8428 (mtp85) REVERT: I 115 GLU cc_start: 0.8839 (mp0) cc_final: 0.8532 (mp0) REVERT: I 121 ASN cc_start: 0.9009 (t0) cc_final: 0.8702 (t0) REVERT: J 12 SER cc_start: 0.9097 (OUTLIER) cc_final: 0.8623 (t) REVERT: J 54 ASP cc_start: 0.8817 (t70) cc_final: 0.8409 (t0) REVERT: J 101 ASP cc_start: 0.8197 (t0) cc_final: 0.7772 (t0) REVERT: J 107 ASP cc_start: 0.8307 (m-30) cc_final: 0.8101 (m-30) REVERT: J 150 LYS cc_start: 0.9249 (mmmm) cc_final: 0.8870 (mmmt) REVERT: J 164 GLU cc_start: 0.8997 (tp30) cc_final: 0.8601 (tp30) REVERT: L 106 ASP cc_start: 0.8745 (m-30) cc_final: 0.8314 (m-30) REVERT: L 114 ARG cc_start: 0.8888 (mtp-110) cc_final: 0.8657 (ttp-170) REVERT: M 25 GLN cc_start: 0.8755 (tp40) cc_final: 0.8505 (tp40) REVERT: M 95 TYR cc_start: 0.8641 (m-10) cc_final: 0.8406 (m-10) REVERT: M 129 ARG cc_start: 0.8831 (tpt170) cc_final: 0.8442 (tpt170) REVERT: O 71 GLU cc_start: 0.8471 (mp0) cc_final: 0.8214 (mp0) REVERT: O 107 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8209 (tm-30) REVERT: Q 23 ASP cc_start: 0.9190 (OUTLIER) cc_final: 0.8987 (t0) REVERT: Q 25 GLN cc_start: 0.9164 (tp-100) cc_final: 0.8913 (tm-30) REVERT: a 22 ARG cc_start: 0.8765 (ttt180) cc_final: 0.8411 (mtp85) REVERT: a 33 GLN cc_start: 0.7842 (mt0) cc_final: 0.6855 (mm-40) REVERT: a 46 LEU cc_start: 0.8772 (pp) cc_final: 0.8408 (pp) REVERT: a 47 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.7451 (m-10) REVERT: a 64 ASP cc_start: 0.7720 (t0) cc_final: 0.7500 (t0) REVERT: a 123 ASP cc_start: 0.1573 (m-30) cc_final: 0.0940 (t0) REVERT: b 19 GLU cc_start: 0.7612 (tp30) cc_final: 0.5836 (tp30) REVERT: b 54 GLN cc_start: 0.8489 (pp30) cc_final: 0.8224 (pm20) REVERT: b 71 ASP cc_start: 0.8294 (t70) cc_final: 0.8021 (p0) REVERT: b 72 LYS cc_start: 0.5638 (tppt) cc_final: 0.5306 (tppt) REVERT: b 101 GLU cc_start: 0.8322 (pm20) cc_final: 0.7550 (pp20) REVERT: b 109 ARG cc_start: 0.7249 (ptp-110) cc_final: 0.6979 (tpm170) REVERT: b 189 LEU cc_start: 0.7706 (pt) cc_final: 0.6736 (tp) outliers start: 72 outliers final: 57 residues processed: 524 average time/residue: 0.1501 time to fit residues: 118.0281 Evaluate side-chains 534 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 473 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 61 CYS Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 59 CYS Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain I residue 59 CYS Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 125 SER Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 61 CYS Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 158 CYS Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 109 CYS Chi-restraints excluded: chain O residue 121 ASN Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain Q residue 23 ASP Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain Q residue 44 ILE Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 134 MET Chi-restraints excluded: chain Q residue 142 ILE Chi-restraints excluded: chain Q residue 170 ASP Chi-restraints excluded: chain a residue 23 CYS Chi-restraints excluded: chain a residue 25 PHE Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 47 PHE Chi-restraints excluded: chain a residue 63 PHE Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 119 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 169 optimal weight: 0.1980 chunk 171 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 141 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 72 ASN O 121 ASN b 76 ASN b 118 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.100017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.069765 restraints weight = 45448.440| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.18 r_work: 0.2873 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19944 Z= 0.115 Angle : 0.553 8.420 27184 Z= 0.281 Chirality : 0.036 0.157 2997 Planarity : 0.004 0.049 3471 Dihedral : 11.382 88.773 4363 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.24 % Favored : 98.72 % Rotamer: Outliers : 3.29 % Allowed : 26.70 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.97 (0.17), residues: 2426 helix: 2.88 (0.13), residues: 1665 sheet: 0.95 (0.46), residues: 118 loop : -0.37 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 17 TYR 0.014 0.001 TYR A 158 PHE 0.012 0.001 PHE b 48 TRP 0.033 0.001 TRP a 34 HIS 0.006 0.001 HIS C 48 Details of bonding type rmsd covalent geometry : bond 0.00256 (19939) covalent geometry : angle 0.55294 (27174) SS BOND : bond 0.00349 ( 5) SS BOND : angle 0.67380 ( 10) hydrogen bonds : bond 0.03808 ( 1241) hydrogen bonds : angle 3.45951 ( 3657) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 497 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.8815 (ttm110) cc_final: 0.8118 (ttp-110) REVERT: A 115 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8573 (mp0) REVERT: A 144 MET cc_start: 0.8400 (ptp) cc_final: 0.7956 (ptp) REVERT: B 15 LYS cc_start: 0.9208 (mtmm) cc_final: 0.8825 (mppt) REVERT: B 59 MET cc_start: 0.9118 (tmm) cc_final: 0.8706 (ttt) REVERT: B 101 ASP cc_start: 0.8636 (t0) cc_final: 0.8002 (t0) REVERT: B 107 ASP cc_start: 0.8973 (t0) cc_final: 0.8685 (m-30) REVERT: B 118 ILE cc_start: 0.9754 (OUTLIER) cc_final: 0.9450 (pt) REVERT: B 148 GLN cc_start: 0.8746 (mp10) cc_final: 0.8448 (mp10) REVERT: B 170 ASP cc_start: 0.9155 (t0) cc_final: 0.8900 (t0) REVERT: C 53 LYS cc_start: 0.8746 (tttm) cc_final: 0.8172 (tmtt) REVERT: C 57 ASP cc_start: 0.8856 (m-30) cc_final: 0.8417 (m-30) REVERT: C 62 LYS cc_start: 0.9293 (tptp) cc_final: 0.9082 (tptt) REVERT: C 71 GLU cc_start: 0.8795 (mp0) cc_final: 0.8438 (mp0) REVERT: C 107 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8581 (mm-30) REVERT: D 3 ASP cc_start: 0.7975 (p0) cc_final: 0.7739 (p0) REVERT: D 101 ASP cc_start: 0.8719 (t70) cc_final: 0.7750 (t0) REVERT: F 2 LYS cc_start: 0.9028 (tttp) cc_final: 0.8812 (tptp) REVERT: F 62 LYS cc_start: 0.9201 (tppt) cc_final: 0.8713 (tptm) REVERT: F 71 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8157 (mm-30) REVERT: F 74 ASP cc_start: 0.8228 (p0) cc_final: 0.7966 (p0) REVERT: F 114 ARG cc_start: 0.8903 (ttm-80) cc_final: 0.8510 (mtt-85) REVERT: F 151 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8627 (mm-30) REVERT: G 25 GLN cc_start: 0.8722 (mm-40) cc_final: 0.8469 (mm-40) REVERT: G 148 GLN cc_start: 0.8797 (mp10) cc_final: 0.8466 (mp10) REVERT: I 1 MET cc_start: 0.7996 (mmt) cc_final: 0.7689 (mmt) REVERT: I 54 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7716 (mt-10) REVERT: I 102 THR cc_start: 0.7815 (p) cc_final: 0.7214 (p) REVERT: I 106 ASP cc_start: 0.8575 (m-30) cc_final: 0.8293 (m-30) REVERT: I 114 ARG cc_start: 0.8675 (mtp-110) cc_final: 0.8462 (mtp85) REVERT: I 115 GLU cc_start: 0.8829 (mp0) cc_final: 0.8485 (mp0) REVERT: I 121 ASN cc_start: 0.8985 (t0) cc_final: 0.8664 (t0) REVERT: J 54 ASP cc_start: 0.8824 (t70) cc_final: 0.8428 (t0) REVERT: J 101 ASP cc_start: 0.8112 (t0) cc_final: 0.7703 (t0) REVERT: J 150 LYS cc_start: 0.9245 (mmmm) cc_final: 0.8876 (mmmt) REVERT: L 68 ASN cc_start: 0.8980 (m110) cc_final: 0.8739 (p0) REVERT: L 106 ASP cc_start: 0.8717 (m-30) cc_final: 0.8300 (m-30) REVERT: M 25 GLN cc_start: 0.8731 (tp40) cc_final: 0.8487 (tp40) REVERT: M 95 TYR cc_start: 0.8567 (m-10) cc_final: 0.8330 (m-10) REVERT: M 129 ARG cc_start: 0.8790 (tpt170) cc_final: 0.8424 (tpt170) REVERT: O 68 ASN cc_start: 0.8620 (m110) cc_final: 0.8242 (m-40) REVERT: O 71 GLU cc_start: 0.8469 (mp0) cc_final: 0.7746 (mp0) REVERT: O 107 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8175 (tm-30) REVERT: O 122 LEU cc_start: 0.9068 (mt) cc_final: 0.8851 (mp) REVERT: Q 25 GLN cc_start: 0.9168 (tp-100) cc_final: 0.8942 (tm-30) REVERT: a 22 ARG cc_start: 0.8694 (ttt180) cc_final: 0.8337 (mtp85) REVERT: a 33 GLN cc_start: 0.7804 (mt0) cc_final: 0.6817 (mm-40) REVERT: a 47 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7292 (m-10) REVERT: a 56 ASN cc_start: 0.7875 (m-40) cc_final: 0.7521 (m110) REVERT: a 64 ASP cc_start: 0.7688 (t0) cc_final: 0.7478 (t0) REVERT: a 123 ASP cc_start: 0.1510 (m-30) cc_final: 0.0979 (t0) REVERT: b 19 GLU cc_start: 0.7606 (tp30) cc_final: 0.5857 (tp30) REVERT: b 25 LYS cc_start: 0.8752 (ttpt) cc_final: 0.8435 (tptt) REVERT: b 31 ASP cc_start: 0.8563 (p0) cc_final: 0.8362 (p0) REVERT: b 54 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8158 (pm20) REVERT: b 76 ASN cc_start: 0.5323 (m-40) cc_final: 0.4688 (m110) REVERT: b 101 GLU cc_start: 0.8249 (pm20) cc_final: 0.7481 (pp20) REVERT: b 189 LEU cc_start: 0.7689 (pt) cc_final: 0.6699 (tp) outliers start: 64 outliers final: 51 residues processed: 534 average time/residue: 0.1598 time to fit residues: 128.2214 Evaluate side-chains 533 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 478 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 61 CYS Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 59 CYS Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain I residue 59 CYS Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 125 SER Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 158 CYS Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 109 CYS Chi-restraints excluded: chain O residue 121 ASN Chi-restraints excluded: chain Q residue 44 ILE Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 134 MET Chi-restraints excluded: chain Q residue 142 ILE Chi-restraints excluded: chain a residue 4 VAL Chi-restraints excluded: chain a residue 23 CYS Chi-restraints excluded: chain a residue 25 PHE Chi-restraints excluded: chain a residue 47 PHE Chi-restraints excluded: chain a residue 63 PHE Chi-restraints excluded: chain b residue 54 GLN Chi-restraints excluded: chain b residue 119 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 48 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 164 optimal weight: 0.5980 chunk 154 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 222 optimal weight: 7.9990 chunk 226 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 0.0670 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 72 ASN O 121 ASN b 118 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.100358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.070089 restraints weight = 45033.322| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.28 r_work: 0.2887 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19944 Z= 0.116 Angle : 0.564 9.275 27184 Z= 0.288 Chirality : 0.036 0.161 2997 Planarity : 0.004 0.049 3471 Dihedral : 11.225 89.067 4363 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.20 % Favored : 98.76 % Rotamer: Outliers : 3.09 % Allowed : 26.59 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.06 (0.18), residues: 2426 helix: 2.95 (0.13), residues: 1647 sheet: 1.07 (0.46), residues: 118 loop : -0.26 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 114 TYR 0.020 0.001 TYR Q 168 PHE 0.010 0.001 PHE b 48 TRP 0.032 0.001 TRP a 34 HIS 0.006 0.001 HIS C 48 Details of bonding type rmsd covalent geometry : bond 0.00262 (19939) covalent geometry : angle 0.56414 (27174) SS BOND : bond 0.00292 ( 5) SS BOND : angle 0.63738 ( 10) hydrogen bonds : bond 0.03713 ( 1241) hydrogen bonds : angle 3.43363 ( 3657) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 491 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.8550 (ttm110) cc_final: 0.8142 (ttp80) REVERT: A 115 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8481 (mp0) REVERT: A 144 MET cc_start: 0.8427 (ptp) cc_final: 0.7983 (ptp) REVERT: B 15 LYS cc_start: 0.9193 (mtmm) cc_final: 0.8815 (mppt) REVERT: B 59 MET cc_start: 0.9117 (tmm) cc_final: 0.8699 (ttt) REVERT: B 101 ASP cc_start: 0.8633 (t0) cc_final: 0.7990 (t0) REVERT: B 107 ASP cc_start: 0.8978 (t0) cc_final: 0.8692 (m-30) REVERT: B 148 GLN cc_start: 0.8744 (mp10) cc_final: 0.8441 (mp10) REVERT: B 151 MET cc_start: 0.8050 (mmm) cc_final: 0.7516 (mtp) REVERT: B 170 ASP cc_start: 0.9141 (t0) cc_final: 0.8888 (t0) REVERT: C 42 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8671 (tm-30) REVERT: C 53 LYS cc_start: 0.8718 (tttm) cc_final: 0.8213 (tmtt) REVERT: C 57 ASP cc_start: 0.8839 (m-30) cc_final: 0.8397 (m-30) REVERT: C 71 GLU cc_start: 0.8766 (mp0) cc_final: 0.8413 (mp0) REVERT: C 74 ASP cc_start: 0.8930 (p0) cc_final: 0.8574 (p0) REVERT: C 107 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8582 (mm-30) REVERT: D 3 ASP cc_start: 0.7927 (p0) cc_final: 0.7721 (p0) REVERT: D 101 ASP cc_start: 0.8616 (t70) cc_final: 0.7789 (t0) REVERT: F 2 LYS cc_start: 0.9045 (tttp) cc_final: 0.8830 (tptp) REVERT: F 62 LYS cc_start: 0.9206 (tppt) cc_final: 0.8731 (tptm) REVERT: F 71 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8175 (mm-30) REVERT: F 74 ASP cc_start: 0.8186 (p0) cc_final: 0.7925 (p0) REVERT: F 107 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8392 (mt-10) REVERT: F 114 ARG cc_start: 0.8917 (ttm-80) cc_final: 0.8494 (mtt-85) REVERT: F 151 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8639 (mm-30) REVERT: G 25 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8491 (mm-40) REVERT: G 77 ARG cc_start: 0.9091 (ttp80) cc_final: 0.8765 (ttp80) REVERT: G 148 GLN cc_start: 0.8800 (mp10) cc_final: 0.8500 (mp10) REVERT: I 1 MET cc_start: 0.8031 (mmt) cc_final: 0.7697 (mmt) REVERT: I 54 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7711 (mt-10) REVERT: I 102 THR cc_start: 0.7786 (p) cc_final: 0.7190 (p) REVERT: I 106 ASP cc_start: 0.8549 (m-30) cc_final: 0.8259 (m-30) REVERT: I 115 GLU cc_start: 0.8870 (mp0) cc_final: 0.8536 (mp0) REVERT: I 121 ASN cc_start: 0.8948 (t0) cc_final: 0.8628 (t0) REVERT: J 54 ASP cc_start: 0.8859 (t70) cc_final: 0.8479 (t0) REVERT: J 101 ASP cc_start: 0.8024 (t0) cc_final: 0.7638 (t0) REVERT: J 150 LYS cc_start: 0.9237 (mmmm) cc_final: 0.8867 (mmmt) REVERT: J 164 GLU cc_start: 0.9022 (tp30) cc_final: 0.8711 (tp30) REVERT: L 68 ASN cc_start: 0.8991 (m110) cc_final: 0.8774 (p0) REVERT: L 89 TYR cc_start: 0.9204 (m-80) cc_final: 0.8996 (m-10) REVERT: L 106 ASP cc_start: 0.8702 (m-30) cc_final: 0.8281 (m-30) REVERT: M 25 GLN cc_start: 0.8695 (tp40) cc_final: 0.8476 (tp40) REVERT: M 95 TYR cc_start: 0.8546 (m-10) cc_final: 0.8310 (m-10) REVERT: M 115 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8948 (tt0) REVERT: M 129 ARG cc_start: 0.8796 (tpt170) cc_final: 0.8429 (tpt170) REVERT: M 150 LYS cc_start: 0.9045 (tppt) cc_final: 0.8839 (tppt) REVERT: O 68 ASN cc_start: 0.8616 (m110) cc_final: 0.8255 (m-40) REVERT: O 71 GLU cc_start: 0.8446 (mp0) cc_final: 0.7811 (mp0) REVERT: O 107 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8573 (mt-10) REVERT: O 122 LEU cc_start: 0.9079 (mt) cc_final: 0.8863 (mp) REVERT: Q 25 GLN cc_start: 0.9164 (tp-100) cc_final: 0.8941 (tm-30) REVERT: Q 148 GLN cc_start: 0.8572 (mp10) cc_final: 0.8159 (mp10) REVERT: a 22 ARG cc_start: 0.8698 (ttt180) cc_final: 0.8340 (mtp85) REVERT: a 33 GLN cc_start: 0.7836 (mt0) cc_final: 0.6960 (mm110) REVERT: a 47 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7439 (m-10) REVERT: a 56 ASN cc_start: 0.7828 (m-40) cc_final: 0.7470 (m110) REVERT: a 64 ASP cc_start: 0.7738 (t0) cc_final: 0.7526 (t0) REVERT: a 123 ASP cc_start: 0.1537 (m-30) cc_final: 0.0974 (t0) REVERT: b 19 GLU cc_start: 0.7558 (tp30) cc_final: 0.5816 (tp30) REVERT: b 25 LYS cc_start: 0.8729 (ttpt) cc_final: 0.8390 (tptt) REVERT: b 101 GLU cc_start: 0.8253 (pm20) cc_final: 0.7506 (pp20) REVERT: b 189 LEU cc_start: 0.7745 (pt) cc_final: 0.6747 (tp) outliers start: 60 outliers final: 47 residues processed: 524 average time/residue: 0.1583 time to fit residues: 124.6382 Evaluate side-chains 530 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 481 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 61 CYS Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 59 CYS Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain I residue 59 CYS Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 125 SER Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 158 CYS Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 109 CYS Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain Q residue 44 ILE Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 134 MET Chi-restraints excluded: chain Q residue 142 ILE Chi-restraints excluded: chain a residue 4 VAL Chi-restraints excluded: chain a residue 23 CYS Chi-restraints excluded: chain a residue 25 PHE Chi-restraints excluded: chain a residue 47 PHE Chi-restraints excluded: chain a residue 63 PHE Chi-restraints excluded: chain b residue 119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 133 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 132 optimal weight: 0.6980 chunk 191 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 129 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN D 72 ASN ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 30 ASN O 121 ASN Q 72 ASN ** b 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 118 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.099793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.069228 restraints weight = 45545.744| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.25 r_work: 0.2871 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19944 Z= 0.125 Angle : 0.577 8.159 27184 Z= 0.294 Chirality : 0.037 0.169 2997 Planarity : 0.004 0.048 3471 Dihedral : 11.146 88.831 4363 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.15 % Favored : 98.80 % Rotamer: Outliers : 2.83 % Allowed : 27.31 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.05 (0.17), residues: 2426 helix: 2.91 (0.13), residues: 1665 sheet: 1.10 (0.46), residues: 118 loop : -0.26 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG a 30 TYR 0.027 0.001 TYR b 34 PHE 0.010 0.001 PHE b 120 TRP 0.031 0.001 TRP a 34 HIS 0.006 0.001 HIS C 48 Details of bonding type rmsd covalent geometry : bond 0.00287 (19939) covalent geometry : angle 0.57703 (27174) SS BOND : bond 0.00283 ( 5) SS BOND : angle 0.59536 ( 10) hydrogen bonds : bond 0.03822 ( 1241) hydrogen bonds : angle 3.44754 ( 3657) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4852 Ramachandran restraints generated. 2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 481 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8425 (pm20) cc_final: 0.8145 (pm20) REVERT: A 114 ARG cc_start: 0.8597 (ttm110) cc_final: 0.8170 (ttp80) REVERT: A 115 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8495 (mp0) REVERT: A 144 MET cc_start: 0.8431 (ptp) cc_final: 0.7983 (ptp) REVERT: B 15 LYS cc_start: 0.9187 (mtmm) cc_final: 0.8808 (mppt) REVERT: B 59 MET cc_start: 0.9126 (tmm) cc_final: 0.8717 (ttt) REVERT: B 101 ASP cc_start: 0.8539 (t0) cc_final: 0.7904 (t0) REVERT: B 107 ASP cc_start: 0.8978 (t0) cc_final: 0.8693 (m-30) REVERT: B 148 GLN cc_start: 0.8742 (mp10) cc_final: 0.8443 (mp10) REVERT: B 151 MET cc_start: 0.8049 (mmm) cc_final: 0.7541 (mtp) REVERT: B 170 ASP cc_start: 0.9145 (t0) cc_final: 0.8893 (t0) REVERT: C 42 GLU cc_start: 0.9005 (tm-30) cc_final: 0.8674 (tm-30) REVERT: C 53 LYS cc_start: 0.8670 (tttm) cc_final: 0.8230 (tmtt) REVERT: C 57 ASP cc_start: 0.8810 (m-30) cc_final: 0.8465 (m-30) REVERT: C 71 GLU cc_start: 0.8770 (mp0) cc_final: 0.8443 (mp0) REVERT: C 74 ASP cc_start: 0.8964 (p0) cc_final: 0.8613 (p0) REVERT: C 107 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8552 (mm-30) REVERT: D 3 ASP cc_start: 0.7978 (p0) cc_final: 0.7754 (p0) REVERT: D 101 ASP cc_start: 0.8645 (t70) cc_final: 0.7723 (t0) REVERT: F 2 LYS cc_start: 0.9051 (tttp) cc_final: 0.8838 (tptp) REVERT: F 39 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8187 (tm-30) REVERT: F 62 LYS cc_start: 0.9212 (tppt) cc_final: 0.8770 (tptm) REVERT: F 71 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8163 (mm-30) REVERT: F 74 ASP cc_start: 0.8193 (p0) cc_final: 0.7931 (p0) REVERT: F 114 ARG cc_start: 0.8961 (ttm-80) cc_final: 0.8557 (mtt-85) REVERT: F 151 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8650 (mm-30) REVERT: G 25 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8475 (mm-40) REVERT: G 148 GLN cc_start: 0.8836 (mp10) cc_final: 0.8496 (mp10) REVERT: I 1 MET cc_start: 0.8059 (mmt) cc_final: 0.7710 (mmt) REVERT: I 54 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7708 (mt-10) REVERT: I 102 THR cc_start: 0.7819 (p) cc_final: 0.6701 (p) REVERT: I 106 ASP cc_start: 0.8564 (m-30) cc_final: 0.8111 (m-30) REVERT: I 115 GLU cc_start: 0.8874 (mp0) cc_final: 0.8523 (mp0) REVERT: I 121 ASN cc_start: 0.8968 (t0) cc_final: 0.8616 (t0) REVERT: J 54 ASP cc_start: 0.8879 (t70) cc_final: 0.8514 (t0) REVERT: J 101 ASP cc_start: 0.8038 (t0) cc_final: 0.7646 (t0) REVERT: J 150 LYS cc_start: 0.9236 (mmmm) cc_final: 0.8864 (mmmt) REVERT: J 164 GLU cc_start: 0.8997 (tp30) cc_final: 0.8696 (tp30) REVERT: L 68 ASN cc_start: 0.8972 (m110) cc_final: 0.8760 (p0) REVERT: L 89 TYR cc_start: 0.9225 (m-80) cc_final: 0.8996 (m-10) REVERT: L 106 ASP cc_start: 0.8736 (m-30) cc_final: 0.8303 (m-30) REVERT: L 118 ARG cc_start: 0.9013 (ttp-170) cc_final: 0.8430 (ttp-170) REVERT: M 25 GLN cc_start: 0.8690 (tp40) cc_final: 0.8459 (tp40) REVERT: M 95 TYR cc_start: 0.8572 (m-10) cc_final: 0.8313 (m-10) REVERT: M 115 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8981 (tt0) REVERT: M 129 ARG cc_start: 0.8814 (tpt170) cc_final: 0.8434 (tpt170) REVERT: M 150 LYS cc_start: 0.9054 (tppt) cc_final: 0.8822 (tppt) REVERT: O 68 ASN cc_start: 0.8664 (m110) cc_final: 0.8312 (m-40) REVERT: O 71 GLU cc_start: 0.8438 (mp0) cc_final: 0.7823 (mp0) REVERT: O 107 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8171 (tm-30) REVERT: O 114 ARG cc_start: 0.8716 (mmm-85) cc_final: 0.8349 (mmm-85) REVERT: O 122 LEU cc_start: 0.9095 (mt) cc_final: 0.8889 (mp) REVERT: Q 148 GLN cc_start: 0.8556 (mp10) cc_final: 0.8140 (mp10) REVERT: a 22 ARG cc_start: 0.8675 (ttt180) cc_final: 0.8374 (mtp85) REVERT: a 33 GLN cc_start: 0.7879 (mt0) cc_final: 0.6983 (mm-40) REVERT: a 47 PHE cc_start: 0.8191 (OUTLIER) cc_final: 0.7469 (m-10) REVERT: a 123 ASP cc_start: 0.1620 (m-30) cc_final: 0.0952 (t0) REVERT: b 19 GLU cc_start: 0.7638 (tp30) cc_final: 0.5917 (tp30) REVERT: b 25 LYS cc_start: 0.8762 (ttpt) cc_final: 0.8428 (tptt) REVERT: b 189 LEU cc_start: 0.7803 (pt) cc_final: 0.6798 (tp) outliers start: 55 outliers final: 47 residues processed: 511 average time/residue: 0.1567 time to fit residues: 120.2282 Evaluate side-chains 525 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 476 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 61 CYS Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 59 CYS Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain I residue 59 CYS Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 125 SER Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 158 CYS Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 109 CYS Chi-restraints excluded: chain O residue 121 ASN Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain Q residue 44 ILE Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 134 MET Chi-restraints excluded: chain Q residue 142 ILE Chi-restraints excluded: chain a residue 4 VAL Chi-restraints excluded: chain a residue 23 CYS Chi-restraints excluded: chain a residue 25 PHE Chi-restraints excluded: chain a residue 47 PHE Chi-restraints excluded: chain a residue 63 PHE Chi-restraints excluded: chain b residue 119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 235 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 232 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 222 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 116 optimal weight: 0.0670 chunk 191 optimal weight: 4.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 72 ASN O 121 ASN ** b 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 118 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.099705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.069369 restraints weight = 45654.429| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.29 r_work: 0.2871 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.5184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19944 Z= 0.127 Angle : 0.584 8.010 27184 Z= 0.297 Chirality : 0.037 0.163 2997 Planarity : 0.004 0.048 3471 Dihedral : 11.109 88.772 4363 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.28 % Favored : 98.68 % Rotamer: Outliers : 2.78 % Allowed : 27.37 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.05 (0.17), residues: 2426 helix: 2.91 (0.13), residues: 1665 sheet: 1.15 (0.47), residues: 118 loop : -0.28 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 137 TYR 0.016 0.001 TYR b 214 PHE 0.010 0.001 PHE F 60 TRP 0.029 0.001 TRP a 34 HIS 0.008 0.001 HIS b 30 Details of bonding type rmsd covalent geometry : bond 0.00290 (19939) covalent geometry : angle 0.58409 (27174) SS BOND : bond 0.00273 ( 5) SS BOND : angle 0.59572 ( 10) hydrogen bonds : bond 0.03826 ( 1241) hydrogen bonds : angle 3.45286 ( 3657) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5651.55 seconds wall clock time: 97 minutes 26.00 seconds (5846.00 seconds total)