Starting phenix.real_space_refine on Sat Jul 4 17:56:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tap_25780/07_2026/7tap_25780.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tap_25780/07_2026/7tap_25780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tap_25780/07_2026/7tap_25780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tap_25780/07_2026/7tap_25780.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tap_25780/07_2026/7tap_25780.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tap_25780/07_2026/7tap_25780.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tap_25780/07_2026/7tap_25780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tap_25780/07_2026/7tap_25780.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.325 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 143 5.16 5 C 14821 2.51 5 N 3558 2.21 5 O 3998 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22520 Number of models: 1 Model: "" Number of chains: 22 Chain: "D" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1145 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 151} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1473 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 195} Chain: "N" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 400 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 50} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 570 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 66} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "O" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 529 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "F" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "J" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "K" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "L" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2802 Classifications: {'peptide': 345} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 335} Chain: "A" Number of atoms: 6089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 6089 Classifications: {'peptide': 750} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 728} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'KJL': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'KJL': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'KJL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'KJL': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'KJL': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'KJL': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'KJL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.54, per 1000 atoms: 0.20 Number of scatterers: 22520 At special positions: 0 Unit cell: (123.6, 121.54, 133.9, 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 143 16.00 O 3998 8.00 N 3558 7.00 C 14821 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 17 " - pdb=" SG CYS E 75 " distance=2.08 Simple disulfide: pdb=" SG CYS F 17 " - pdb=" SG CYS F 75 " distance=2.05 Simple disulfide: pdb=" SG CYS G 17 " - pdb=" SG CYS G 75 " distance=2.06 Simple disulfide: pdb=" SG CYS H 17 " - pdb=" SG CYS H 75 " distance=2.07 Simple disulfide: pdb=" SG CYS I 17 " - pdb=" SG CYS I 75 " distance=2.05 Simple disulfide: pdb=" SG CYS J 17 " - pdb=" SG CYS J 75 " distance=2.07 Simple disulfide: pdb=" SG CYS K 17 " - pdb=" SG CYS K 75 " distance=2.05 Simple disulfide: pdb=" SG CYS L 17 " - pdb=" SG CYS L 75 " distance=2.10 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 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5252 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 7 sheets defined 79.7% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'D' and resid 14 through 50 removed outlier: 3.840A pdb=" N PHE D 18 " --> pdb=" O TYR D 14 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 56 removed outlier: 6.107A pdb=" N GLU D 54 " --> pdb=" O PHE D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 59 No H-bonds generated for 'chain 'D' and resid 57 through 59' Processing helix chain 'D' and resid 60 through 83 removed outlier: 3.521A pdb=" N LEU D 69 " --> pdb=" O MET D 65 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA D 70 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN D 83 " --> pdb=" O LEU D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 127 Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 133 through 164 removed outlier: 3.536A pdb=" N LEU D 147 " --> pdb=" O PHE D 143 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY D 148 " --> pdb=" O SER D 144 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU D 164 " --> pdb=" O THR D 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 39 Processing helix chain 'C' and resid 41 through 45 Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 55 through 91 removed outlier: 3.559A pdb=" N TRP C 59 " --> pdb=" O SER C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 100 removed outlier: 3.986A pdb=" N LYS C 99 " --> pdb=" O ARG C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 123 removed outlier: 3.826A pdb=" N ILE C 104 " --> pdb=" O ASN C 100 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL C 110 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA C 111 " --> pdb=" O CYS C 107 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 177 Processing helix chain 'C' and resid 179 through 206 removed outlier: 4.272A pdb=" N LYS C 183 " --> pdb=" O ALA C 179 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL C 186 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE C 193 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU C 194 " --> pdb=" O PHE C 190 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY C 195 " --> pdb=" O GLY C 191 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU C 196 " --> pdb=" O SER C 192 " (cutoff:3.500A) Processing helix chain 'N' and resid 220 through 246 Processing helix chain 'N' and resid 250 through 254 removed outlier: 3.722A pdb=" N ALA N 253 " --> pdb=" O THR N 250 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 25 removed outlier: 3.756A pdb=" N VAL M 7 " --> pdb=" O SER M 3 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 55 removed outlier: 3.787A pdb=" N GLN M 55 " --> pdb=" O THR M 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 44 removed outlier: 4.066A pdb=" N PHE E 12 " --> pdb=" O TYR E 8 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE E 21 " --> pdb=" O CYS E 17 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL E 44 " --> pdb=" O CYS E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 49 through 54 Processing helix chain 'E' and resid 54 through 76 removed outlier: 3.614A pdb=" N ILE E 63 " --> pdb=" O MET E 59 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA E 64 " --> pdb=" O ALA E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 120 Processing helix chain 'E' and resid 124 through 152 removed outlier: 4.186A pdb=" N GLY E 128 " --> pdb=" O ARG E 124 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU E 139 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY E 140 " --> pdb=" O ALA E 136 " (cutoff:3.500A) Processing helix chain 'O' and resid 8 through 33 removed outlier: 4.234A pdb=" N GLY O 20 " --> pdb=" O LEU O 16 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE O 23 " --> pdb=" O PHE O 19 " (cutoff:3.500A) Processing helix chain 'O' and resid 35 through 40 Processing helix chain 'O' and resid 47 through 75 removed outlier: 3.962A pdb=" N VAL O 51 " --> pdb=" O ASP O 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 44 removed outlier: 4.156A pdb=" N PHE F 12 " --> pdb=" O TYR F 8 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY F 13 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE F 21 " --> pdb=" O CYS F 17 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR F 24 " --> pdb=" O ALA F 20 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL F 44 " --> pdb=" O CYS F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 50 Processing helix chain 'F' and resid 54 through 76 removed outlier: 3.752A pdb=" N ILE F 63 " --> pdb=" O MET F 59 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA F 64 " --> pdb=" O ALA F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 120 Processing helix chain 'F' and resid 124 through 155 removed outlier: 4.235A pdb=" N GLY F 128 " --> pdb=" O ARG F 124 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY F 140 " --> pdb=" O ALA F 136 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY F 143 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG F 153 " --> pdb=" O LEU F 149 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR F 155 " --> pdb=" O ASN F 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 44 removed outlier: 4.110A pdb=" N PHE G 12 " --> pdb=" O TYR G 8 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY G 13 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE G 21 " --> pdb=" O CYS G 17 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL G 44 " --> pdb=" O CYS G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 50 Processing helix chain 'G' and resid 54 through 76 removed outlier: 3.659A pdb=" N ILE G 63 " --> pdb=" O MET G 59 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 120 Processing helix chain 'G' and resid 124 through 155 removed outlier: 4.284A pdb=" N GLY G 128 " --> pdb=" O ARG G 124 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU G 139 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY G 140 " --> pdb=" O ALA G 136 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ARG G 153 " --> pdb=" O LEU G 149 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR G 155 " --> pdb=" O ASN G 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 44 removed outlier: 4.106A pdb=" N PHE H 12 " --> pdb=" O TYR H 8 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY H 13 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE H 21 " --> pdb=" O CYS H 17 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL H 44 " --> pdb=" O CYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 50 Processing helix chain 'H' and resid 54 through 77 removed outlier: 3.670A pdb=" N ILE H 63 " --> pdb=" O MET H 59 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA H 64 " --> pdb=" O ALA H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 120 Processing helix chain 'H' and resid 122 through 124 No H-bonds generated for 'chain 'H' and resid 122 through 124' Processing helix chain 'H' and resid 125 through 155 removed outlier: 3.703A pdb=" N LEU H 139 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY H 140 " --> pdb=" O ALA H 136 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU H 141 " --> pdb=" O GLU H 137 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG H 153 " --> pdb=" O LEU H 149 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR H 155 " --> pdb=" O ASN H 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 43 removed outlier: 4.086A pdb=" N PHE I 12 " --> pdb=" O TYR I 8 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY I 13 " --> pdb=" O ALA I 9 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE I 21 " --> pdb=" O CYS I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 50 Processing helix chain 'I' and resid 51 through 53 No H-bonds generated for 'chain 'I' and resid 51 through 53' Processing helix chain 'I' and resid 54 through 77 removed outlier: 3.941A pdb=" N ILE I 63 " --> pdb=" O MET I 59 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA I 64 " --> pdb=" O ALA I 60 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU I 73 " --> pdb=" O VAL I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 120 Processing helix chain 'I' and resid 124 through 155 removed outlier: 4.141A pdb=" N GLY I 128 " --> pdb=" O ARG I 124 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU I 139 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY I 140 " --> pdb=" O ALA I 136 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG I 153 " --> pdb=" O LEU I 149 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR I 155 " --> pdb=" O ASN I 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 44 removed outlier: 4.114A pdb=" N PHE J 12 " --> pdb=" O TYR J 8 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY J 13 " --> pdb=" O ALA J 9 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE J 21 " --> pdb=" O CYS J 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL J 44 " --> pdb=" O CYS J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 50 Processing helix chain 'J' and resid 54 through 76 removed outlier: 4.000A pdb=" N ILE J 63 " --> pdb=" O MET J 59 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA J 64 " --> pdb=" O ALA J 60 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR J 76 " --> pdb=" O VAL J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 120 Processing helix chain 'J' and resid 124 through 155 removed outlier: 4.199A pdb=" N GLY J 128 " --> pdb=" O ARG J 124 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY J 140 " --> pdb=" O ALA J 136 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG J 153 " --> pdb=" O LEU J 149 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR J 155 " --> pdb=" O ASN J 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 8 through 44 removed outlier: 4.072A pdb=" N PHE K 12 " --> pdb=" O TYR K 8 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY K 13 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE K 21 " --> pdb=" O CYS K 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL K 44 " --> pdb=" O CYS K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 50 Processing helix chain 'K' and resid 54 through 77 removed outlier: 3.768A pdb=" N ILE K 63 " --> pdb=" O MET K 59 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA K 64 " --> pdb=" O ALA K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 120 removed outlier: 3.606A pdb=" N ALA K 103 " --> pdb=" O LEU K 99 " (cutoff:3.500A) Processing helix chain 'K' and resid 124 through 155 removed outlier: 4.176A pdb=" N GLY K 128 " --> pdb=" O ARG K 124 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU K 139 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY K 140 " --> pdb=" O ALA K 136 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ARG K 153 " --> pdb=" O LEU K 149 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR K 155 " --> pdb=" O ASN K 151 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 44 removed outlier: 4.120A pdb=" N PHE L 12 " --> pdb=" O TYR L 8 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY L 13 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE L 21 " --> pdb=" O CYS L 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL L 44 " --> pdb=" O CYS L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 50 Processing helix chain 'L' and resid 54 through 76 Processing helix chain 'L' and resid 83 through 120 Processing helix chain 'L' and resid 124 through 155 removed outlier: 4.083A pdb=" N GLY L 128 " --> pdb=" O ARG L 124 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE L 135 " --> pdb=" O LEU L 131 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU L 139 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY L 140 " --> pdb=" O ALA L 136 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR L 155 " --> pdb=" O ASN L 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 7 removed outlier: 4.219A pdb=" N ASN B 7 " --> pdb=" O GLY B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 23 Processing helix chain 'B' and resid 26 through 35 Processing helix chain 'B' and resid 38 through 48 removed outlier: 3.595A pdb=" N SER B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 86 Processing helix chain 'B' and resid 89 through 116 removed outlier: 4.006A pdb=" N GLY B 101 " --> pdb=" O TYR B 97 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR B 102 " --> pdb=" O ILE B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 136 through 141 removed outlier: 3.655A pdb=" N VAL B 141 " --> pdb=" O THR B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 152 Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'B' and resid 173 through 199 Processing helix chain 'B' and resid 203 through 230 removed outlier: 3.734A pdb=" N GLN B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER B 230 " --> pdb=" O ASN B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 240 Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 261 through 272 removed outlier: 3.814A pdb=" N ASN B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL B 272 " --> pdb=" O ALA B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 276 removed outlier: 3.946A pdb=" N ARG B 276 " --> pdb=" O TYR B 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 273 through 276' Processing helix chain 'B' and resid 283 through 300 Processing helix chain 'B' and resid 306 through 332 removed outlier: 3.968A pdb=" N TRP B 310 " --> pdb=" O ILE B 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 37 removed outlier: 4.404A pdb=" N ARG A 27 " --> pdb=" O GLN A 23 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ASP A 28 " --> pdb=" O GLU A 24 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR A 31 " --> pdb=" O ARG A 27 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 53 removed outlier: 3.603A pdb=" N ARG A 53 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 79 Processing helix chain 'A' and resid 103 through 147 Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 193 through 208 removed outlier: 4.161A pdb=" N ALA A 197 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N THR A 198 " --> pdb=" O ASP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 266 through 325 removed outlier: 4.106A pdb=" N GLU A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASP A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N SER A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 361 removed outlier: 4.317A pdb=" N ALA A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N THR A 348 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 398 removed outlier: 4.558A pdb=" N PHE A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TYR A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 398 " --> pdb=" O CYS A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 424 removed outlier: 4.489A pdb=" N VAL A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Proline residue: A 416 - end of helix Processing helix chain 'A' and resid 425 through 442 removed outlier: 3.536A pdb=" N LEU A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 449 Processing helix chain 'A' and resid 452 through 461 Processing helix chain 'A' and resid 461 through 480 Processing helix chain 'A' and resid 519 through 523 removed outlier: 3.848A pdb=" N TRP A 522 " --> pdb=" O ASP A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 562 Processing helix chain 'A' and resid 564 through 571 Processing helix chain 'A' and resid 571 through 596 removed outlier: 3.610A pdb=" N GLY A 575 " --> pdb=" O ASN A 571 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 582 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR A 585 " --> pdb=" O GLY A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 602 Processing helix chain 'A' and resid 607 through 618 removed outlier: 3.621A pdb=" N PHE A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 659 Proline residue: A 646 - end of helix removed outlier: 5.176A pdb=" N LYS A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Proline residue: A 653 - end of helix Processing helix chain 'A' and resid 707 through 733 removed outlier: 3.913A pdb=" N VAL A 727 " --> pdb=" O CYS A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 755 Processing helix chain 'A' and resid 756 through 761 Processing helix chain 'A' and resid 762 through 784 Processing helix chain 'A' and resid 787 through 803 Processing helix chain 'A' and resid 805 through 810 removed outlier: 4.054A pdb=" N PHE A 809 " --> pdb=" O SER A 805 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'M' and resid 63 through 64 Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 41 removed outlier: 4.213A pdb=" N ILE A 334 " --> pdb=" O ASP A 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 40 through 41 removed outlier: 4.221A pdb=" N LEU A 16 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 214 through 217 removed outlier: 4.358A pdb=" N THR A 188 " --> pdb=" O TYR A 261 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 222 through 224 Processing sheet with id=AA6, first strand: chain 'A' and resid 378 through 379 Processing sheet with id=AA7, first strand: chain 'A' and resid 494 through 495 1778 hydrogen bonds defined for protein. 5208 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.43 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 3501 1.27 - 1.41: 5746 1.41 - 1.55: 13358 1.55 - 1.69: 167 1.69 - 1.82: 204 Bond restraints: 22976 Sorted by residual: bond pdb=" C SER G 96 " pdb=" O SER G 96 " ideal model delta sigma weight residual 1.236 1.135 0.101 1.16e-02 7.43e+03 7.62e+01 bond pdb=" C LEU I 141 " pdb=" O LEU I 141 " ideal model delta sigma weight residual 1.237 1.135 0.102 1.17e-02 7.31e+03 7.54e+01 bond pdb=" C ILE G 134 " pdb=" O ILE G 134 " ideal model delta sigma weight residual 1.237 1.141 0.097 1.17e-02 7.31e+03 6.83e+01 bond pdb=" C ILE K 134 " pdb=" O ILE K 134 " ideal model delta sigma weight residual 1.237 1.140 0.096 1.19e-02 7.06e+03 6.57e+01 bond pdb=" C ILE E 134 " pdb=" O ILE E 134 " ideal model delta sigma weight residual 1.237 1.142 0.095 1.19e-02 7.06e+03 6.38e+01 ... (remaining 22971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 28771 2.90 - 5.81: 2185 5.81 - 8.71: 207 8.71 - 11.62: 37 11.62 - 14.52: 2 Bond angle restraints: 31202 Sorted by residual: angle pdb=" CA ALA F 20 " pdb=" C ALA F 20 " pdb=" O ALA F 20 " ideal model delta sigma weight residual 120.82 112.05 8.77 1.05e+00 9.07e-01 6.98e+01 angle pdb=" CA ALA H 20 " pdb=" C ALA H 20 " pdb=" O ALA H 20 " ideal model delta sigma weight residual 120.82 112.49 8.33 1.05e+00 9.07e-01 6.30e+01 angle pdb=" CA ALA E 20 " pdb=" C ALA E 20 " pdb=" O ALA E 20 " ideal model delta sigma weight residual 120.82 112.68 8.14 1.05e+00 9.07e-01 6.01e+01 angle pdb=" N LEU L 68 " pdb=" CA LEU L 68 " pdb=" C LEU L 68 " ideal model delta sigma weight residual 112.23 102.59 9.64 1.26e+00 6.30e-01 5.86e+01 angle pdb=" CA GLU G 137 " pdb=" C GLU G 137 " pdb=" N VAL G 138 " ideal model delta sigma weight residual 117.30 125.78 -8.48 1.16e+00 7.43e-01 5.34e+01 ... (remaining 31197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 12066 17.98 - 35.96: 946 35.96 - 53.94: 193 53.94 - 71.93: 52 71.93 - 89.91: 37 Dihedral angle restraints: 13294 sinusoidal: 5020 harmonic: 8274 Sorted by residual: dihedral pdb=" CB CYS I 17 " pdb=" SG CYS I 17 " pdb=" SG CYS I 75 " pdb=" CB CYS I 75 " ideal model delta sinusoidal sigma weight residual -86.00 -167.40 81.40 1 1.00e+01 1.00e-02 8.16e+01 dihedral pdb=" CB CYS E 17 " pdb=" SG CYS E 17 " pdb=" SG CYS E 75 " pdb=" CB CYS E 75 " ideal model delta sinusoidal sigma weight residual -86.00 -165.14 79.14 1 1.00e+01 1.00e-02 7.79e+01 dihedral pdb=" CB CYS G 17 " pdb=" SG CYS G 17 " pdb=" SG CYS G 75 " pdb=" CB CYS G 75 " ideal model delta sinusoidal sigma weight residual -86.00 -129.63 43.63 1 1.00e+01 1.00e-02 2.65e+01 ... (remaining 13291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2950 0.074 - 0.148: 570 0.148 - 0.223: 145 0.223 - 0.297: 28 0.297 - 0.371: 18 Chirality restraints: 3711 Sorted by residual: chirality pdb=" CB THR I 24 " pdb=" CA THR I 24 " pdb=" OG1 THR I 24 " pdb=" CG2 THR I 24 " both_signs ideal model delta sigma weight residual False 2.55 2.18 0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" C09 KJL F 201 " pdb=" C08 KJL F 201 " pdb=" C10 KJL F 201 " pdb=" O48 KJL F 201 " both_signs ideal model delta sigma weight residual False -2.38 -2.74 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" C09 KJL E 201 " pdb=" C08 KJL E 201 " pdb=" C10 KJL E 201 " pdb=" O48 KJL E 201 " both_signs ideal model delta sigma weight residual False -2.38 -2.74 0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 3708 not shown) Planarity restraints: 3879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY G 67 " 0.025 2.00e-02 2.50e+03 5.18e-02 2.68e+01 pdb=" C GLY G 67 " -0.090 2.00e-02 2.50e+03 pdb=" O GLY G 67 " 0.033 2.00e-02 2.50e+03 pdb=" N LEU G 68 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY K 67 " -0.025 2.00e-02 2.50e+03 5.10e-02 2.60e+01 pdb=" C GLY K 67 " 0.088 2.00e-02 2.50e+03 pdb=" O GLY K 67 " -0.033 2.00e-02 2.50e+03 pdb=" N LEU K 68 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER L 71 " -0.023 2.00e-02 2.50e+03 4.88e-02 2.38e+01 pdb=" C SER L 71 " 0.084 2.00e-02 2.50e+03 pdb=" O SER L 71 " -0.032 2.00e-02 2.50e+03 pdb=" N VAL L 72 " -0.029 2.00e-02 2.50e+03 ... (remaining 3876 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3468 2.76 - 3.30: 24187 3.30 - 3.83: 40448 3.83 - 4.37: 52195 4.37 - 4.90: 85086 Nonbonded interactions: 205384 Sorted by model distance: nonbonded pdb=" OG SER B 315 " pdb=" OH TYR B 345 " model vdw 2.225 3.040 nonbonded pdb=" OH TYR A 116 " pdb=" NH1 ARG A 120 " model vdw 2.238 3.120 nonbonded pdb=" O LEU A 38 " pdb=" OH TYR A 817 " model vdw 2.240 3.040 nonbonded pdb=" O LEU N 254 " pdb=" NE2 GLN K 121 " model vdw 2.250 3.120 nonbonded pdb=" O ASP A 224 " pdb=" N ARG A 228 " model vdw 2.251 3.120 ... (remaining 205379 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 'E' and resid 1 through 159) selection = (chain 'F' and resid 1 through 159) selection = (chain 'G' and resid 1 through 159) selection = (chain 'H' and resid 1 through 159) selection = (chain 'I' and resid 1 through 159) selection = (chain 'J' and resid 1 through 159) selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.090 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 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 : 0.013 0.134 22984 Z= 0.847 Angle : 1.487 18.114 31218 Z= 1.035 Chirality : 0.069 0.371 3711 Planarity : 0.008 0.084 3879 Dihedral : 14.585 89.908 8018 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.28 % Favored : 98.65 % Rotamer: Outliers : 1.37 % Allowed : 3.59 % Favored : 95.05 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 2.35 % 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 are not related in a simple way. whole: 0.26 (0.15), residues: 2881 helix: 0.31 (0.11), residues: 2131 sheet: -0.63 (0.78), residues: 42 loop : 0.24 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 153 TYR 0.026 0.002 TYR F 66 PHE 0.029 0.002 PHE L 23 TRP 0.029 0.002 TRP B 312 HIS 0.009 0.001 HIS A 801 Details of bonding type rmsd/Z covalent geometry : bond 0.01269 / 0.85 (22976) covalent geometry : angle 1.47335 / 1.03 (31202) SS BOND : bond 0.03939 / 2.68 ( 8) SS BOND : angle 9.06549 / 6.63 ( 16) hydrogen bonds : bond 0.18438 / 12.32 ( 1776) hydrogen bonds : angle 7.73298 / 5.62 ( 5208) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 328 time to evaluate : 0.782 Fit side-chains REVERT: D 40 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.7730 (tttp) REVERT: C 134 TYR cc_start: 0.8927 (m-80) cc_final: 0.8605 (m-80) REVERT: M 43 MET cc_start: 0.7303 (mtp) cc_final: 0.7023 (mtp) REVERT: G 19 SER cc_start: 0.8750 (m) cc_final: 0.8421 (m) REVERT: G 58 ILE cc_start: 0.8746 (mt) cc_final: 0.8325 (mt) REVERT: G 59 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8495 (mmt) REVERT: H 59 MET cc_start: 0.8748 (mmt) cc_final: 0.8010 (mmt) REVERT: H 131 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7929 (tp) REVERT: J 59 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.8040 (mmm) REVERT: L 30 TYR cc_start: 0.8676 (t80) cc_final: 0.8472 (t80) REVERT: B 185 TYR cc_start: 0.7498 (OUTLIER) cc_final: 0.7283 (m-80) REVERT: B 186 LYS cc_start: 0.8377 (tttm) cc_final: 0.8017 (tttt) REVERT: B 194 ASN cc_start: 0.7340 (m-40) cc_final: 0.6849 (m-40) outliers start: 32 outliers final: 3 residues processed: 350 average time/residue: 0.5084 time to fit residues: 208.0020 Evaluate side-chains 268 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 260 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain F residue 59 MET Chi-restraints excluded: chain G residue 59 MET Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain J residue 59 MET Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain B residue 185 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN I 80 GLN K 82 GLN K 151 ASN B 332 GLN A 210 ASN A 442 ASN A 499 HIS A 533 ASN A 634 GLN A 796 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.147749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.111075 restraints weight = 21427.562| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.34 r_work: 0.3108 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22984 Z= 0.179 Angle : 0.574 7.203 31218 Z= 0.303 Chirality : 0.040 0.153 3711 Planarity : 0.004 0.059 3879 Dihedral : 7.284 84.957 3293 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.08 % Favored : 98.89 % Rotamer: Outliers : 2.31 % Allowed : 8.97 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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 are not related in a simple way. whole: 1.65 (0.15), residues: 2881 helix: 1.53 (0.11), residues: 2148 sheet: -0.63 (0.77), residues: 42 loop : -0.02 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 205 TYR 0.015 0.001 TYR D 127 PHE 0.029 0.002 PHE C 80 TRP 0.016 0.001 TRP A 737 HIS 0.005 0.001 HIS A 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (22976) covalent geometry : angle 0.57222 / 0.30 (31202) SS BOND : bond 0.00455 / 0.26 ( 8) SS BOND : angle 1.88992 / 1.38 ( 16) hydrogen bonds : bond 0.05375 / 3.59 ( 1776) hydrogen bonds : angle 4.62513 / 3.42 ( 5208) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 299 time to evaluate : 0.692 Fit side-chains REVERT: D 94 ASN cc_start: 0.8622 (t0) cc_final: 0.8407 (t160) REVERT: C 134 TYR cc_start: 0.9043 (m-80) cc_final: 0.8757 (m-80) REVERT: K 127 VAL cc_start: 0.8646 (t) cc_final: 0.8440 (m) REVERT: L 30 TYR cc_start: 0.9002 (t80) cc_final: 0.8778 (t80) REVERT: B 145 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7270 (tp) REVERT: B 175 MET cc_start: 0.6497 (mmm) cc_final: 0.5893 (mpp) REVERT: B 185 TYR cc_start: 0.8218 (OUTLIER) cc_final: 0.7979 (m-80) REVERT: B 194 ASN cc_start: 0.7739 (m-40) cc_final: 0.7195 (m-40) REVERT: B 258 GLN cc_start: 0.7416 (mp10) cc_final: 0.6929 (mt0) REVERT: B 313 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8350 (tpt) REVERT: B 334 GLN cc_start: 0.7665 (mp10) cc_final: 0.7301 (mt0) REVERT: A 195 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.6950 (mtpp) REVERT: A 371 LEU cc_start: 0.8127 (tp) cc_final: 0.7920 (mt) REVERT: A 426 MET cc_start: 0.8506 (mtp) cc_final: 0.8282 (mtp) REVERT: A 804 GLU cc_start: 0.8505 (mp0) cc_final: 0.8220 (mp0) outliers start: 54 outliers final: 14 residues processed: 337 average time/residue: 0.4954 time to fit residues: 194.9877 Evaluate side-chains 273 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 255 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 82 GLN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 753 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 249 optimal weight: 1.9990 chunk 280 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 180 optimal weight: 0.8980 chunk 179 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 217 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN A 210 ASN A 442 ASN A 499 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.143531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.106686 restraints weight = 21696.303| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.33 r_work: 0.3086 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 22984 Z= 0.162 Angle : 0.518 8.391 31218 Z= 0.273 Chirality : 0.039 0.150 3711 Planarity : 0.004 0.049 3879 Dihedral : 6.474 79.975 3275 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.32 % Favored : 98.65 % Rotamer: Outliers : 2.82 % Allowed : 11.49 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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 are not related in a simple way. whole: 1.91 (0.15), residues: 2881 helix: 1.75 (0.11), residues: 2149 sheet: -0.62 (0.76), residues: 42 loop : -0.03 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 205 TYR 0.012 0.001 TYR E 142 PHE 0.027 0.002 PHE C 80 TRP 0.013 0.001 TRP A 737 HIS 0.004 0.001 HIS A 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (22976) covalent geometry : angle 0.51445 / 0.27 (31202) SS BOND : bond 0.00558 / 0.27 ( 8) SS BOND : angle 2.63523 / 1.64 ( 16) hydrogen bonds : bond 0.05118 / 3.44 ( 1776) hydrogen bonds : angle 4.50375 / 3.32 ( 5208) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 283 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: D 23 CYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8444 (m) REVERT: D 94 ASN cc_start: 0.8576 (t0) cc_final: 0.8360 (t160) REVERT: C 134 TYR cc_start: 0.9058 (m-80) cc_final: 0.8762 (m-80) REVERT: E 99 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8575 (mm) REVERT: O 36 GLU cc_start: 0.7868 (tt0) cc_final: 0.7619 (tt0) REVERT: H 99 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8410 (mm) REVERT: K 82 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8608 (pt0) REVERT: K 127 VAL cc_start: 0.8662 (t) cc_final: 0.8429 (m) REVERT: L 30 TYR cc_start: 0.9072 (t80) cc_final: 0.8859 (t80) REVERT: B 175 MET cc_start: 0.6519 (mmm) cc_final: 0.5859 (mpp) REVERT: B 194 ASN cc_start: 0.7717 (m-40) cc_final: 0.7164 (m-40) REVERT: B 258 GLN cc_start: 0.7566 (mp10) cc_final: 0.7335 (mp10) REVERT: B 313 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8336 (tpt) REVERT: A 23 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.7058 (tt0) REVERT: A 195 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.6979 (mtpp) REVERT: A 426 MET cc_start: 0.8506 (mtp) cc_final: 0.8304 (mtp) REVERT: A 746 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8451 (mp) REVERT: A 761 PHE cc_start: 0.7492 (m-10) cc_final: 0.7121 (m-10) REVERT: A 799 ARG cc_start: 0.8765 (tmt90) cc_final: 0.8149 (tmt170) REVERT: A 804 GLU cc_start: 0.8701 (mp0) cc_final: 0.8246 (mp0) REVERT: A 806 MET cc_start: 0.8819 (mtp) cc_final: 0.8602 (mtp) outliers start: 66 outliers final: 23 residues processed: 323 average time/residue: 0.5423 time to fit residues: 203.1815 Evaluate side-chains 290 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 259 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain L residue 17 CYS Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 753 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 93 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 218 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 261 optimal weight: 0.5980 chunk 231 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 94 ASN C 46 ASN ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 151 ASN ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN A 442 ASN A 499 HIS A 533 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.141961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.104522 restraints weight = 21949.362| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.35 r_work: 0.3111 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 22984 Z= 0.261 Angle : 0.600 8.627 31218 Z= 0.311 Chirality : 0.043 0.211 3711 Planarity : 0.004 0.048 3879 Dihedral : 6.540 83.391 3273 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.60 % Favored : 98.37 % Rotamer: Outliers : 2.78 % Allowed : 12.25 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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 are not related in a simple way. whole: 1.60 (0.15), residues: 2881 helix: 1.54 (0.11), residues: 2142 sheet: -0.71 (0.82), residues: 36 loop : -0.16 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 205 TYR 0.015 0.002 TYR G 76 PHE 0.029 0.002 PHE C 80 TRP 0.014 0.002 TRP A 340 HIS 0.007 0.001 HIS D 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.26 (22976) covalent geometry : angle 0.59591 / 0.31 (31202) SS BOND : bond 0.00528 / 0.34 ( 8) SS BOND : angle 3.14075 / 2.28 ( 16) hydrogen bonds : bond 0.05625 / 3.78 ( 1776) hydrogen bonds : angle 4.74953 / 3.51 ( 5208) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 287 time to evaluate : 0.865 Fit side-chains REVERT: D 23 CYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8592 (m) REVERT: C 86 MET cc_start: 0.8872 (mtp) cc_final: 0.8530 (ttm) REVERT: E 124 ARG cc_start: 0.8621 (mtp180) cc_final: 0.8367 (mtp180) REVERT: G 82 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8467 (pp30) REVERT: G 125 LEU cc_start: 0.8238 (tp) cc_final: 0.8015 (tt) REVERT: G 131 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7485 (mp) REVERT: H 157 ASP cc_start: 0.7325 (OUTLIER) cc_final: 0.7009 (t70) REVERT: J 3 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7308 (tt0) REVERT: K 131 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8229 (mm) REVERT: B 145 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7202 (tp) REVERT: B 181 ARG cc_start: 0.7672 (tmm-80) cc_final: 0.7163 (ttm-80) REVERT: B 194 ASN cc_start: 0.7758 (m-40) cc_final: 0.7141 (m-40) REVERT: B 313 MET cc_start: 0.8673 (mmm) cc_final: 0.8331 (tpt) REVERT: A 124 MET cc_start: 0.7613 (mtt) cc_final: 0.7385 (mtt) REVERT: A 195 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7141 (mtpp) REVERT: A 426 MET cc_start: 0.8604 (mtp) cc_final: 0.8363 (mtp) REVERT: A 746 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8506 (mp) REVERT: A 799 ARG cc_start: 0.8826 (tmt90) cc_final: 0.8533 (tmt90) outliers start: 65 outliers final: 24 residues processed: 329 average time/residue: 0.5390 time to fit residues: 207.3334 Evaluate side-chains 304 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 271 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 3 GLU Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 134 ILE Chi-restraints excluded: chain L residue 145 ILE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 753 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 68 optimal weight: 1.9990 chunk 158 optimal weight: 0.5980 chunk 216 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 240 optimal weight: 1.9990 chunk 280 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 219 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 159 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN K 82 GLN K 151 ASN ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN B 258 GLN A 210 ASN A 499 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.152421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.116722 restraints weight = 21606.588| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.30 r_work: 0.3017 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22984 Z= 0.171 Angle : 0.511 8.188 31218 Z= 0.269 Chirality : 0.039 0.158 3711 Planarity : 0.004 0.046 3879 Dihedral : 6.117 83.427 3273 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.46 % Favored : 98.51 % Rotamer: Outliers : 2.56 % Allowed : 14.05 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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 are not related in a simple way. whole: 1.71 (0.15), residues: 2881 helix: 1.55 (0.11), residues: 2189 sheet: -0.69 (0.82), residues: 36 loop : 0.01 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 205 TYR 0.013 0.001 TYR A 186 PHE 0.024 0.001 PHE C 80 TRP 0.012 0.001 TRP A 737 HIS 0.005 0.001 HIS A 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (22976) covalent geometry : angle 0.50976 / 0.27 (31202) SS BOND : bond 0.00286 / 0.20 ( 8) SS BOND : angle 1.77430 / 1.25 ( 16) hydrogen bonds : bond 0.05120 / 3.45 ( 1776) hydrogen bonds : angle 4.57743 / 3.39 ( 5208) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 281 time to evaluate : 0.831 Fit side-chains REVERT: D 23 CYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8507 (m) REVERT: C 86 MET cc_start: 0.8857 (mtp) cc_final: 0.8401 (ttm) REVERT: C 134 TYR cc_start: 0.9090 (m-80) cc_final: 0.8867 (m-80) REVERT: E 50 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7380 (tt) REVERT: G 82 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8570 (pp30) REVERT: K 45 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8575 (mt) REVERT: K 131 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8227 (mm) REVERT: B 145 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7223 (tp) REVERT: B 181 ARG cc_start: 0.7705 (tmm-80) cc_final: 0.7091 (ttm-80) REVERT: B 194 ASN cc_start: 0.7742 (m-40) cc_final: 0.7133 (m-40) REVERT: B 258 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7824 (mp10) REVERT: B 313 MET cc_start: 0.8625 (mmm) cc_final: 0.8283 (tpt) REVERT: A 195 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7082 (mtpp) REVERT: A 426 MET cc_start: 0.8636 (mtp) cc_final: 0.8293 (mtp) REVERT: A 746 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8505 (mp) REVERT: A 799 ARG cc_start: 0.8822 (tmt90) cc_final: 0.8357 (tmt170) outliers start: 60 outliers final: 26 residues processed: 315 average time/residue: 0.5346 time to fit residues: 197.5231 Evaluate side-chains 303 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 268 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 134 ILE Chi-restraints excluded: chain L residue 145 ILE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 753 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 197 optimal weight: 4.9990 chunk 266 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 256 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 230 optimal weight: 0.9980 chunk 188 optimal weight: 0.0060 chunk 61 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 46 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 GLN K 82 GLN ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN A 210 ASN A 499 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.154315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.118781 restraints weight = 21844.078| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.32 r_work: 0.3081 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22984 Z= 0.142 Angle : 0.495 10.407 31218 Z= 0.262 Chirality : 0.038 0.188 3711 Planarity : 0.004 0.044 3879 Dihedral : 5.880 79.354 3273 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.35 % Favored : 98.61 % Rotamer: Outliers : 2.73 % Allowed : 14.56 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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 are not related in a simple way. whole: 1.94 (0.15), residues: 2881 helix: 1.71 (0.11), residues: 2192 sheet: -0.84 (0.79), residues: 38 loop : 0.09 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 205 TYR 0.020 0.001 TYR L 66 PHE 0.024 0.001 PHE C 80 TRP 0.012 0.001 TRP A 737 HIS 0.004 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (22976) covalent geometry : angle 0.49179 / 0.26 (31202) SS BOND : bond 0.00205 / 0.13 ( 8) SS BOND : angle 2.36256 / 1.24 ( 16) hydrogen bonds : bond 0.04898 / 3.29 ( 1776) hydrogen bonds : angle 4.46261 / 3.30 ( 5208) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 287 time to evaluate : 0.747 Fit side-chains REVERT: D 23 CYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8448 (m) REVERT: C 134 TYR cc_start: 0.9069 (m-80) cc_final: 0.8780 (m-80) REVERT: E 50 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7372 (tt) REVERT: O 36 GLU cc_start: 0.7861 (tt0) cc_final: 0.7569 (tt0) REVERT: G 82 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8737 (pt0) REVERT: L 59 MET cc_start: 0.8082 (mtt) cc_final: 0.7830 (mtt) REVERT: B 145 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7296 (tp) REVERT: B 181 ARG cc_start: 0.7746 (tmm-80) cc_final: 0.7182 (ttm-80) REVERT: B 194 ASN cc_start: 0.7768 (m-40) cc_final: 0.7196 (m-40) REVERT: B 274 GLU cc_start: 0.7757 (mp0) cc_final: 0.7497 (mp0) REVERT: B 313 MET cc_start: 0.8635 (mmm) cc_final: 0.8336 (tpt) REVERT: A 126 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7398 (p0) REVERT: A 195 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7117 (mtpp) REVERT: A 426 MET cc_start: 0.8663 (mtp) cc_final: 0.8363 (mtp) REVERT: A 746 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8525 (mp) outliers start: 64 outliers final: 20 residues processed: 326 average time/residue: 0.5265 time to fit residues: 201.7212 Evaluate side-chains 300 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 273 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 129 MET Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 746 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 81 optimal weight: 0.9990 chunk 211 optimal weight: 0.9980 chunk 5 optimal weight: 0.0980 chunk 213 optimal weight: 0.6980 chunk 226 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 220 optimal weight: 0.9990 chunk 236 optimal weight: 0.7980 chunk 276 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 72 GLN ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN A 210 ASN A 499 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.154746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.119233 restraints weight = 21582.259| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.32 r_work: 0.3152 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22984 Z= 0.143 Angle : 0.494 9.565 31218 Z= 0.260 Chirality : 0.038 0.170 3711 Planarity : 0.004 0.044 3879 Dihedral : 5.693 68.133 3273 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.46 % Favored : 98.51 % Rotamer: Outliers : 2.31 % Allowed : 15.37 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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 are not related in a simple way. whole: 2.00 (0.15), residues: 2881 helix: 1.77 (0.11), residues: 2187 sheet: -0.88 (0.79), residues: 38 loop : 0.08 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 153 TYR 0.026 0.001 TYR L 66 PHE 0.024 0.001 PHE C 80 TRP 0.013 0.001 TRP A 204 HIS 0.004 0.000 HIS A 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (22976) covalent geometry : angle 0.49205 / 0.26 (31202) SS BOND : bond 0.00178 / 0.10 ( 8) SS BOND : angle 2.19173 / 1.20 ( 16) hydrogen bonds : bond 0.04825 / 3.25 ( 1776) hydrogen bonds : angle 4.41896 / 3.27 ( 5208) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 292 time to evaluate : 0.855 Fit side-chains REVERT: D 23 CYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8429 (m) REVERT: C 86 MET cc_start: 0.8858 (mtp) cc_final: 0.8395 (ttm) REVERT: C 134 TYR cc_start: 0.9077 (m-80) cc_final: 0.8781 (m-80) REVERT: N 246 ASN cc_start: 0.8776 (OUTLIER) cc_final: 0.8440 (m110) REVERT: N 247 LEU cc_start: 0.8504 (mt) cc_final: 0.8302 (tp) REVERT: E 50 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7252 (tt) REVERT: O 36 GLU cc_start: 0.7831 (tt0) cc_final: 0.7625 (tt0) REVERT: O 53 HIS cc_start: 0.7890 (t-90) cc_final: 0.7687 (t70) REVERT: G 82 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8650 (pt0) REVERT: B 145 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7322 (tp) REVERT: B 181 ARG cc_start: 0.7780 (tmm-80) cc_final: 0.7204 (ttm-80) REVERT: B 194 ASN cc_start: 0.7774 (m-40) cc_final: 0.7206 (m-40) REVERT: B 274 GLU cc_start: 0.7734 (mp0) cc_final: 0.7527 (mp0) REVERT: A 195 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7156 (mtpp) REVERT: A 201 GLN cc_start: 0.7827 (tp40) cc_final: 0.7034 (mt0) REVERT: A 426 MET cc_start: 0.8668 (mtp) cc_final: 0.8342 (mtp) REVERT: A 746 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8534 (mp) outliers start: 54 outliers final: 28 residues processed: 327 average time/residue: 0.5081 time to fit residues: 195.2655 Evaluate side-chains 315 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 280 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain N residue 246 ASN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 129 MET Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 746 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 123 optimal weight: 2.9990 chunk 227 optimal weight: 0.7980 chunk 130 optimal weight: 0.5980 chunk 235 optimal weight: 0.9990 chunk 263 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 218 optimal weight: 0.8980 chunk 265 optimal weight: 0.7980 chunk 97 optimal weight: 0.0770 chunk 212 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN B 258 GLN A 210 ASN A 499 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.152423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.117370 restraints weight = 21721.692| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.30 r_work: 0.3277 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22984 Z= 0.140 Angle : 0.495 9.098 31218 Z= 0.259 Chirality : 0.038 0.155 3711 Planarity : 0.004 0.043 3879 Dihedral : 5.432 51.519 3273 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.46 % Favored : 98.51 % Rotamer: Outliers : 2.13 % Allowed : 16.01 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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 are not related in a simple way. whole: 2.07 (0.15), residues: 2881 helix: 1.83 (0.11), residues: 2187 sheet: -0.89 (0.79), residues: 38 loop : 0.10 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 352 TYR 0.027 0.001 TYR L 66 PHE 0.028 0.001 PHE A 774 TRP 0.017 0.001 TRP A 204 HIS 0.003 0.000 HIS A 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (22976) covalent geometry : angle 0.49292 / 0.26 (31202) SS BOND : bond 0.00117 / 0.07 ( 8) SS BOND : angle 2.16978 / 1.26 ( 16) hydrogen bonds : bond 0.04782 / 3.22 ( 1776) hydrogen bonds : angle 4.38275 / 3.25 ( 5208) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 293 time to evaluate : 0.830 Fit side-chains REVERT: D 23 CYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8355 (m) REVERT: C 134 TYR cc_start: 0.9053 (m-80) cc_final: 0.8761 (m-80) REVERT: N 247 LEU cc_start: 0.8460 (mt) cc_final: 0.8258 (tp) REVERT: E 50 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7228 (tt) REVERT: O 36 GLU cc_start: 0.7786 (tt0) cc_final: 0.7581 (tt0) REVERT: G 82 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8632 (pt0) REVERT: G 125 LEU cc_start: 0.8251 (tp) cc_final: 0.8041 (tt) REVERT: L 46 ARG cc_start: 0.8573 (mmm-85) cc_final: 0.8173 (mtp180) REVERT: B 145 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7288 (tp) REVERT: B 175 MET cc_start: 0.6384 (mmp) cc_final: 0.6120 (mmm) REVERT: B 181 ARG cc_start: 0.7732 (tmm-80) cc_final: 0.7137 (ttm-80) REVERT: B 194 ASN cc_start: 0.7730 (m-40) cc_final: 0.7169 (m-40) REVERT: B 274 GLU cc_start: 0.7748 (mp0) cc_final: 0.7537 (mp0) REVERT: A 195 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7136 (mtpp) REVERT: A 426 MET cc_start: 0.8604 (mtp) cc_final: 0.8258 (mtp) REVERT: A 442 ASN cc_start: 0.7721 (m110) cc_final: 0.7181 (p0) REVERT: A 746 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8487 (mp) REVERT: A 753 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7533 (mmm) outliers start: 50 outliers final: 27 residues processed: 324 average time/residue: 0.5091 time to fit residues: 193.1451 Evaluate side-chains 315 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 281 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 129 MET Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 753 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 62 optimal weight: 5.9990 chunk 258 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 229 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 157 optimal weight: 0.0000 chunk 234 optimal weight: 0.6980 chunk 215 optimal weight: 10.0000 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 ASN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN A 210 ASN A 499 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.152752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.117759 restraints weight = 21847.324| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.31 r_work: 0.3174 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22984 Z= 0.139 Angle : 0.495 8.651 31218 Z= 0.259 Chirality : 0.038 0.147 3711 Planarity : 0.004 0.042 3879 Dihedral : 5.235 49.458 3273 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.35 % Favored : 98.61 % Rotamer: Outliers : 1.96 % Allowed : 16.31 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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 are not related in a simple way. whole: 2.12 (0.15), residues: 2881 helix: 1.86 (0.11), residues: 2187 sheet: -0.94 (0.78), residues: 38 loop : 0.14 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 205 TYR 0.030 0.001 TYR L 66 PHE 0.028 0.001 PHE A 774 TRP 0.023 0.001 TRP A 204 HIS 0.003 0.000 HIS A 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (22976) covalent geometry : angle 0.49296 / 0.26 (31202) SS BOND : bond 0.00133 / 0.08 ( 8) SS BOND : angle 2.14707 / 1.23 ( 16) hydrogen bonds : bond 0.04748 / 3.20 ( 1776) hydrogen bonds : angle 4.36236 / 3.23 ( 5208) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 281 time to evaluate : 0.804 Fit side-chains REVERT: D 23 CYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8377 (m) REVERT: C 134 TYR cc_start: 0.9049 (m-80) cc_final: 0.8773 (m-80) REVERT: N 247 LEU cc_start: 0.8468 (mt) cc_final: 0.8261 (tp) REVERT: E 50 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7256 (tt) REVERT: G 82 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8651 (pt0) REVERT: G 125 LEU cc_start: 0.8283 (tp) cc_final: 0.8070 (tt) REVERT: J 3 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7570 (tt0) REVERT: L 46 ARG cc_start: 0.8599 (mmm-85) cc_final: 0.8213 (mtp180) REVERT: B 145 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7306 (tp) REVERT: B 175 MET cc_start: 0.6386 (mmp) cc_final: 0.6140 (mmm) REVERT: B 178 GLU cc_start: 0.7062 (tp30) cc_final: 0.5857 (tt0) REVERT: B 181 ARG cc_start: 0.7748 (tmm-80) cc_final: 0.6955 (ttm-80) REVERT: B 194 ASN cc_start: 0.7745 (m-40) cc_final: 0.7210 (m-40) REVERT: B 274 GLU cc_start: 0.7711 (mp0) cc_final: 0.7505 (mp0) REVERT: A 126 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7494 (p0) REVERT: A 195 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7138 (mtpp) REVERT: A 426 MET cc_start: 0.8644 (mtp) cc_final: 0.8291 (mtp) REVERT: A 746 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8549 (mp) REVERT: A 753 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7571 (mmm) REVERT: A 761 PHE cc_start: 0.7355 (m-10) cc_final: 0.7072 (m-10) outliers start: 46 outliers final: 28 residues processed: 311 average time/residue: 0.5038 time to fit residues: 182.8576 Evaluate side-chains 312 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 276 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 129 MET Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 753 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 57 optimal weight: 1.9990 chunk 259 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 268 optimal weight: 0.6980 chunk 196 optimal weight: 0.1980 chunk 76 optimal weight: 2.9990 chunk 200 optimal weight: 0.6980 chunk 190 optimal weight: 0.9990 chunk 226 optimal weight: 0.6980 chunk 193 optimal weight: 0.6980 chunk 275 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN A 210 ASN A 499 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.156396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.120749 restraints weight = 21809.018| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.33 r_work: 0.3213 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22984 Z= 0.136 Angle : 0.493 8.356 31218 Z= 0.258 Chirality : 0.038 0.166 3711 Planarity : 0.004 0.042 3879 Dihedral : 5.124 48.984 3273 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.39 % Favored : 98.58 % Rotamer: Outliers : 1.79 % Allowed : 16.82 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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 are not related in a simple way. whole: 2.16 (0.15), residues: 2881 helix: 1.89 (0.11), residues: 2187 sheet: -1.05 (0.76), residues: 38 loop : 0.14 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 352 TYR 0.031 0.001 TYR L 66 PHE 0.025 0.001 PHE A 774 TRP 0.027 0.001 TRP A 204 HIS 0.003 0.000 HIS A 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (22976) covalent geometry : angle 0.49076 / 0.26 (31202) SS BOND : bond 0.00126 / 0.09 ( 8) SS BOND : angle 2.06863 / 1.18 ( 16) hydrogen bonds : bond 0.04693 / 3.16 ( 1776) hydrogen bonds : angle 4.33669 / 3.21 ( 5208) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 286 time to evaluate : 0.652 Fit side-chains REVERT: D 23 CYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8363 (m) REVERT: C 134 TYR cc_start: 0.9041 (m-80) cc_final: 0.8771 (m-80) REVERT: E 50 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7248 (tt) REVERT: G 82 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8747 (pt0) REVERT: G 125 LEU cc_start: 0.8282 (tp) cc_final: 0.8071 (tt) REVERT: J 3 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7563 (tt0) REVERT: L 46 ARG cc_start: 0.8596 (mmm-85) cc_final: 0.8216 (mtp180) REVERT: B 145 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7318 (tp) REVERT: B 150 GLU cc_start: 0.7320 (mm-30) cc_final: 0.7096 (mm-30) REVERT: B 175 MET cc_start: 0.6377 (mmp) cc_final: 0.6150 (mmm) REVERT: B 178 GLU cc_start: 0.7041 (tp30) cc_final: 0.5834 (tt0) REVERT: B 181 ARG cc_start: 0.7740 (tmm-80) cc_final: 0.6947 (ttm-80) REVERT: B 194 ASN cc_start: 0.7733 (m-40) cc_final: 0.7204 (m-40) REVERT: A 126 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7544 (p0) REVERT: A 195 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7132 (mtpp) REVERT: A 247 LYS cc_start: 0.8267 (tppt) cc_final: 0.8052 (tppp) REVERT: A 426 MET cc_start: 0.8641 (mtp) cc_final: 0.8283 (mtp) REVERT: A 442 ASN cc_start: 0.7727 (m110) cc_final: 0.7266 (p0) REVERT: A 746 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8527 (mp) REVERT: A 753 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7548 (mmm) REVERT: A 787 LEU cc_start: 0.7820 (mp) cc_final: 0.7603 (mt) outliers start: 42 outliers final: 29 residues processed: 313 average time/residue: 0.5109 time to fit residues: 186.3507 Evaluate side-chains 309 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 272 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 129 MET Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 753 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 65 optimal weight: 0.5980 chunk 133 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 246 optimal weight: 1.9990 chunk 224 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 237 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 266 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 GLN K 82 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN B 258 GLN A 210 ASN A 499 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.152348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.117183 restraints weight = 21913.318| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.31 r_work: 0.3095 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22984 Z= 0.151 Angle : 0.507 8.643 31218 Z= 0.265 Chirality : 0.038 0.157 3711 Planarity : 0.004 0.042 3879 Dihedral : 5.150 47.705 3273 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.49 % Favored : 98.47 % Rotamer: Outliers : 1.79 % Allowed : 17.04 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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 are not related in a simple way. whole: 2.10 (0.15), residues: 2881 helix: 1.85 (0.11), residues: 2187 sheet: -1.11 (0.76), residues: 38 loop : 0.12 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 276 TYR 0.033 0.001 TYR L 66 PHE 0.025 0.001 PHE A 774 TRP 0.032 0.001 TRP A 204 HIS 0.004 0.001 HIS A 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (22976) covalent geometry : angle 0.50486 / 0.26 (31202) SS BOND : bond 0.00150 / 0.10 ( 8) SS BOND : angle 2.21230 / 1.28 ( 16) hydrogen bonds : bond 0.04798 / 3.23 ( 1776) hydrogen bonds : angle 4.38821 / 3.25 ( 5208) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6553.13 seconds wall clock time: 113 minutes 5.00 seconds (6785.00 seconds total)