Starting phenix.real_space_refine on Thu Mar 5 12:52:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tap_25780/03_2026/7tap_25780.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tap_25780/03_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_25780/03_2026/7tap_25780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tap_25780/03_2026/7tap_25780.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tap_25780/03_2026/7tap_25780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tap_25780/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 4.41, 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: 1.89 Conformation dependent library (CDL) restraints added in 1.0 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: 0.40 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: 4.12 Time building geometry restraints manager: 2.50 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 - 24.54: 12878 24.54 - 49.07: 608 49.07 - 73.61: 118 73.61 - 98.14: 38 98.14 - 122.68: 4 Dihedral angle restraints: 13646 sinusoidal: 5372 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 13643 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: 1.730 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: 0.410 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.980 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 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 : 15.279 122.681 8370 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 covalent geometry : bond 0.01269 (22976) covalent geometry : angle 1.47335 (31202) SS BOND : bond 0.03939 ( 8) SS BOND : angle 9.06549 ( 16) hydrogen bonds : bond 0.18438 ( 1776) hydrogen bonds : angle 7.73298 ( 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 : 0.788 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: 0.5353 time to fit residues: 217.7962 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 : 0.828 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.145104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.108387 restraints weight = 21593.851| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.33 r_work: 0.3109 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22984 Z= 0.174 Angle : 0.577 6.974 31218 Z= 0.303 Chirality : 0.040 0.151 3711 Planarity : 0.004 0.059 3879 Dihedral : 10.019 120.714 3645 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.11 % Favored : 98.85 % Rotamer: Outliers : 2.35 % Allowed : 8.97 % Favored : 88.68 % 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: 1.66 (0.15), residues: 2881 helix: 1.54 (0.11), residues: 2148 sheet: -0.65 (0.77), residues: 42 loop : -0.01 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 205 TYR 0.016 0.001 TYR D 127 PHE 0.030 0.002 PHE C 80 TRP 0.017 0.001 TRP A 737 HIS 0.005 0.001 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00390 (22976) covalent geometry : angle 0.57525 (31202) SS BOND : bond 0.00320 ( 8) SS BOND : angle 2.06095 ( 16) hydrogen bonds : bond 0.05407 ( 1776) hydrogen bonds : angle 4.63789 ( 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 354 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 299 time to evaluate : 0.803 Fit side-chains REVERT: C 134 TYR cc_start: 0.9042 (m-80) cc_final: 0.8761 (m-80) REVERT: K 127 VAL cc_start: 0.8654 (t) cc_final: 0.8446 (m) REVERT: K 138 VAL cc_start: 0.8205 (OUTLIER) cc_final: 0.7995 (p) REVERT: L 30 TYR cc_start: 0.9008 (t80) cc_final: 0.8796 (t80) REVERT: B 145 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7267 (tp) REVERT: B 185 TYR cc_start: 0.8225 (OUTLIER) cc_final: 0.7970 (m-80) REVERT: B 194 ASN cc_start: 0.7731 (m-40) cc_final: 0.7181 (m-40) REVERT: B 258 GLN cc_start: 0.7493 (mp10) cc_final: 0.7024 (mt0) REVERT: B 313 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8361 (tpt) REVERT: B 334 GLN cc_start: 0.7662 (mp10) cc_final: 0.7296 (mt0) REVERT: A 195 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.6954 (mtpp) REVERT: A 371 LEU cc_start: 0.8142 (tp) cc_final: 0.7931 (mt) REVERT: A 746 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8391 (mp) REVERT: A 804 GLU cc_start: 0.8501 (mp0) cc_final: 0.8226 (mp0) outliers start: 55 outliers final: 14 residues processed: 337 average time/residue: 0.5281 time to fit residues: 207.5070 Evaluate side-chains 278 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 258 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 K residue 138 VAL 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 90 SER 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 746 LEU 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: 0.6980 chunk 61 optimal weight: 1.9990 chunk 180 optimal weight: 0.5980 chunk 179 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 217 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 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 K 151 ASN ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN A 210 ASN A 442 ASN A 499 HIS A 533 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.144382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.107654 restraints weight = 21653.359| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.33 r_work: 0.3112 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 22984 Z= 0.156 Angle : 0.520 8.351 31218 Z= 0.273 Chirality : 0.039 0.222 3711 Planarity : 0.004 0.049 3879 Dihedral : 9.295 112.670 3628 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.32 % Favored : 98.65 % Rotamer: Outliers : 2.56 % Allowed : 11.83 % Favored : 85.61 % 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: 1.95 (0.15), residues: 2881 helix: 1.78 (0.11), residues: 2149 sheet: -0.63 (0.76), residues: 42 loop : -0.00 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 205 TYR 0.013 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 covalent geometry : bond 0.00344 (22976) covalent geometry : angle 0.51607 (31202) SS BOND : bond 0.00307 ( 8) SS BOND : angle 2.73137 ( 16) hydrogen bonds : bond 0.05053 ( 1776) hydrogen bonds : angle 4.48136 ( 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 348 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 288 time to evaluate : 0.887 Fit side-chains REVERT: D 23 CYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8411 (m) REVERT: C 134 TYR cc_start: 0.9069 (m-80) cc_final: 0.8757 (m-80) REVERT: E 99 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8574 (mm) REVERT: G 52 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7553 (pttm) REVERT: K 82 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8624 (pt0) REVERT: K 127 VAL cc_start: 0.8649 (t) cc_final: 0.8424 (m) REVERT: L 30 TYR cc_start: 0.9060 (t80) cc_final: 0.8835 (t80) REVERT: B 175 MET cc_start: 0.6491 (mmm) cc_final: 0.5836 (mpp) REVERT: B 194 ASN cc_start: 0.7706 (m-40) cc_final: 0.7154 (m-40) REVERT: B 313 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8337 (tpt) REVERT: A 23 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.7060 (tt0) REVERT: A 195 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.6970 (mtpp) REVERT: A 746 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8415 (mp) REVERT: A 761 PHE cc_start: 0.7478 (m-10) cc_final: 0.7104 (m-10) REVERT: A 799 ARG cc_start: 0.8716 (tmt90) cc_final: 0.8101 (tmt170) REVERT: A 804 GLU cc_start: 0.8699 (mp0) cc_final: 0.8269 (mp0) outliers start: 60 outliers final: 16 residues processed: 324 average time/residue: 0.5642 time to fit residues: 211.8757 Evaluate side-chains 285 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 261 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain H residue 54 ILE 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 B residue 34 THR 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 195 LYS Chi-restraints excluded: chain A residue 244 LEU 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: 4.9990 chunk 29 optimal weight: 0.8980 chunk 71 optimal weight: 0.4980 chunk 149 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 261 optimal weight: 0.7980 chunk 231 optimal weight: 0.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** F 82 GLN G 82 GLN ** G 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 A 210 ASN A 442 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 = 0.3576 r_free = 0.3576 target = 0.141909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.104674 restraints weight = 21879.228| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.36 r_work: 0.3022 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22984 Z= 0.188 Angle : 0.537 8.085 31218 Z= 0.279 Chirality : 0.040 0.181 3711 Planarity : 0.004 0.045 3879 Dihedral : 9.062 113.146 3625 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.56 % Favored : 98.40 % Rotamer: Outliers : 2.43 % Allowed : 12.77 % Favored : 84.80 % 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: 1.90 (0.15), residues: 2881 helix: 1.77 (0.11), residues: 2144 sheet: -0.69 (0.77), residues: 42 loop : -0.09 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 205 TYR 0.012 0.001 TYR A 186 PHE 0.026 0.002 PHE C 80 TRP 0.012 0.001 TRP A 737 HIS 0.005 0.001 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00433 (22976) covalent geometry : angle 0.53413 (31202) SS BOND : bond 0.00435 ( 8) SS BOND : angle 2.29856 ( 16) hydrogen bonds : bond 0.05193 ( 1776) hydrogen bonds : angle 4.53623 ( 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 338 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 281 time to evaluate : 0.805 Fit side-chains REVERT: D 23 CYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8494 (m) REVERT: H 157 ASP cc_start: 0.7338 (OUTLIER) cc_final: 0.7034 (t0) REVERT: J 3 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7231 (tt0) REVERT: J 59 MET cc_start: 0.8802 (mtp) cc_final: 0.8513 (mmt) REVERT: K 127 VAL cc_start: 0.8669 (t) cc_final: 0.8403 (m) REVERT: B 109 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7985 (tp) REVERT: B 110 MET cc_start: 0.8624 (tpt) cc_final: 0.8201 (tpt) REVERT: B 145 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7207 (tp) REVERT: B 150 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7169 (mm-30) REVERT: B 175 MET cc_start: 0.6509 (mmm) cc_final: 0.5853 (mpp) REVERT: B 181 ARG cc_start: 0.7677 (tmm-80) cc_final: 0.7198 (ttm-80) REVERT: B 194 ASN cc_start: 0.7735 (m-40) cc_final: 0.7148 (m-40) REVERT: B 313 MET cc_start: 0.8615 (mmm) cc_final: 0.8319 (tpt) REVERT: A 23 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7222 (tt0) REVERT: A 124 MET cc_start: 0.7614 (mtt) cc_final: 0.7384 (mtt) REVERT: A 195 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.6993 (mtpp) REVERT: A 746 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8442 (mp) REVERT: A 799 ARG cc_start: 0.8786 (tmt90) cc_final: 0.8495 (tmt90) outliers start: 57 outliers final: 23 residues processed: 313 average time/residue: 0.5421 time to fit residues: 197.0240 Evaluate side-chains 296 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 265 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain F residue 127 VAL 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 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 B residue 34 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 109 LEU 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 23 GLN 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 Chi-restraints excluded: chain A residue 776 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: 3.9990 chunk 216 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 240 optimal weight: 0.9990 chunk 280 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 67 optimal weight: 0.0020 chunk 219 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN ** G 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** ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN A 210 ASN A 442 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 = 0.3607 r_free = 0.3607 target = 0.144203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.106946 restraints weight = 21561.615| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.36 r_work: 0.3121 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22984 Z= 0.159 Angle : 0.502 7.890 31218 Z= 0.264 Chirality : 0.038 0.155 3711 Planarity : 0.004 0.044 3879 Dihedral : 8.713 111.511 3625 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.42 % Favored : 98.54 % Rotamer: Outliers : 2.78 % Allowed : 13.49 % Favored : 83.73 % 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: 2.00 (0.15), residues: 2881 helix: 1.84 (0.11), residues: 2144 sheet: -0.62 (0.82), residues: 36 loop : -0.06 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 205 TYR 0.016 0.001 TYR L 66 PHE 0.025 0.001 PHE C 80 TRP 0.012 0.001 TRP A 737 HIS 0.004 0.001 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00356 (22976) covalent geometry : angle 0.50067 (31202) SS BOND : bond 0.00192 ( 8) SS BOND : angle 1.81876 ( 16) hydrogen bonds : bond 0.04991 ( 1776) hydrogen bonds : angle 4.46557 ( 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 347 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 282 time to evaluate : 0.720 Fit side-chains REVERT: D 23 CYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8464 (m) REVERT: C 86 MET cc_start: 0.8862 (mtp) cc_final: 0.8427 (ttm) REVERT: M 47 MET cc_start: 0.8546 (ttt) cc_final: 0.8326 (tpt) REVERT: B 109 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8056 (tp) REVERT: B 145 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7199 (tp) REVERT: B 181 ARG cc_start: 0.7722 (tmm-80) cc_final: 0.7187 (ttm-80) REVERT: B 194 ASN cc_start: 0.7746 (m-40) cc_final: 0.7150 (m-40) REVERT: B 313 MET cc_start: 0.8640 (mmm) cc_final: 0.8357 (tpt) REVERT: A 195 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7025 (mtpp) REVERT: A 746 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8444 (mp) REVERT: A 799 ARG cc_start: 0.8809 (tmt90) cc_final: 0.8476 (tmt90) outliers start: 65 outliers final: 26 residues processed: 322 average time/residue: 0.5240 time to fit residues: 197.4645 Evaluate side-chains 298 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 267 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 F residue 127 VAL Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 131 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 109 LEU 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 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 Chi-restraints excluded: chain A residue 776 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 197 optimal weight: 6.9990 chunk 266 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 256 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 230 optimal weight: 0.7980 chunk 188 optimal weight: 0.7980 chunk 61 optimal weight: 0.1980 chunk 76 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN O 72 GLN ** G 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** B 244 ASN 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 = 0.3672 r_free = 0.3672 target = 0.149396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.112509 restraints weight = 21696.556| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.37 r_work: 0.3116 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22984 Z= 0.143 Angle : 0.498 10.583 31218 Z= 0.261 Chirality : 0.038 0.190 3711 Planarity : 0.004 0.043 3879 Dihedral : 8.455 111.035 3625 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.28 % Favored : 98.68 % Rotamer: Outliers : 2.39 % Allowed : 14.90 % 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: 2.04 (0.15), residues: 2881 helix: 1.80 (0.11), residues: 2187 sheet: -0.82 (0.80), residues: 38 loop : 0.10 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 153 TYR 0.021 0.001 TYR L 66 PHE 0.024 0.001 PHE C 80 TRP 0.011 0.001 TRP A 737 HIS 0.003 0.000 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00312 (22976) covalent geometry : angle 0.49459 (31202) SS BOND : bond 0.00590 ( 8) SS BOND : angle 2.61757 ( 16) hydrogen bonds : bond 0.04844 ( 1776) hydrogen bonds : angle 4.41031 ( 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 337 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 281 time to evaluate : 0.670 Fit side-chains REVERT: D 23 CYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8441 (m) REVERT: J 3 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7337 (tt0) REVERT: K 127 VAL cc_start: 0.8696 (t) cc_final: 0.8402 (m) REVERT: B 109 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8011 (tp) REVERT: B 145 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7262 (tp) REVERT: B 181 ARG cc_start: 0.7686 (tmm-80) cc_final: 0.7126 (ttm-80) REVERT: B 194 ASN cc_start: 0.7686 (m-40) cc_final: 0.7111 (m-40) REVERT: B 313 MET cc_start: 0.8652 (mmm) cc_final: 0.8353 (tpt) REVERT: A 126 ASP cc_start: 0.7592 (OUTLIER) cc_final: 0.7340 (p0) REVERT: A 195 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7011 (mtpp) REVERT: A 746 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8443 (mp) REVERT: A 799 ARG cc_start: 0.8784 (tmt90) cc_final: 0.8335 (tmt170) outliers start: 56 outliers final: 25 residues processed: 315 average time/residue: 0.5114 time to fit residues: 188.9624 Evaluate side-chains 302 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 270 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 3 GLU 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 134 ILE Chi-restraints excluded: chain L residue 145 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 109 LEU 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 238 VAL Chi-restraints excluded: chain A residue 244 LEU 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 Chi-restraints excluded: chain A residue 776 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 81 optimal weight: 0.7980 chunk 211 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 213 optimal weight: 0.8980 chunk 226 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 220 optimal weight: 5.9990 chunk 236 optimal weight: 0.8980 chunk 276 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 ASN ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN ** 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 ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3750 r_free = 0.3750 target = 0.154493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.118892 restraints weight = 21572.774| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.31 r_work: 0.3054 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 22984 Z= 0.155 Angle : 0.506 9.512 31218 Z= 0.264 Chirality : 0.038 0.171 3711 Planarity : 0.004 0.043 3879 Dihedral : 8.321 111.879 3625 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.46 % Favored : 98.51 % Rotamer: Outliers : 2.31 % Allowed : 15.46 % Favored : 82.24 % 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: 2.01 (0.15), residues: 2881 helix: 1.78 (0.11), residues: 2187 sheet: -0.87 (0.80), residues: 38 loop : 0.08 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 205 TYR 0.026 0.001 TYR L 66 PHE 0.026 0.001 PHE A 774 TRP 0.014 0.001 TRP A 204 HIS 0.004 0.001 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00346 (22976) covalent geometry : angle 0.50280 (31202) SS BOND : bond 0.00139 ( 8) SS BOND : angle 2.55162 ( 16) hydrogen bonds : bond 0.04893 ( 1776) hydrogen bonds : angle 4.42471 ( 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 337 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 283 time to evaluate : 0.785 Fit side-chains REVERT: D 23 CYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8463 (m) REVERT: G 125 LEU cc_start: 0.8250 (tp) cc_final: 0.8027 (tt) REVERT: H 157 ASP cc_start: 0.7199 (OUTLIER) cc_final: 0.6930 (t0) REVERT: B 109 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8060 (tp) REVERT: B 145 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7271 (tp) REVERT: B 181 ARG cc_start: 0.7726 (tmm-80) cc_final: 0.7164 (ttm-80) REVERT: B 194 ASN cc_start: 0.7722 (m-40) cc_final: 0.7137 (m-40) REVERT: A 85 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6875 (mp0) REVERT: A 195 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7111 (mtpp) REVERT: A 746 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8506 (mp) outliers start: 54 outliers final: 26 residues processed: 316 average time/residue: 0.5196 time to fit residues: 192.3812 Evaluate side-chains 306 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 273 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 F residue 127 VAL Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain I residue 131 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 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 109 LEU 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 54 THR Chi-restraints excluded: chain A residue 85 GLU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 123 optimal weight: 2.9990 chunk 227 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 235 optimal weight: 0.9980 chunk 263 optimal weight: 0.1980 chunk 55 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 265 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN A 499 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.151958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.116926 restraints weight = 21756.767| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.30 r_work: 0.3127 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 22984 Z= 0.150 Angle : 0.510 10.763 31218 Z= 0.265 Chirality : 0.038 0.157 3711 Planarity : 0.004 0.042 3879 Dihedral : 8.223 112.220 3625 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.32 % Favored : 98.65 % Rotamer: Outliers : 2.35 % Allowed : 15.67 % Favored : 81.98 % 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: 2.04 (0.15), residues: 2881 helix: 1.80 (0.11), residues: 2187 sheet: -0.85 (0.80), residues: 38 loop : 0.11 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 153 TYR 0.030 0.001 TYR L 66 PHE 0.025 0.001 PHE C 80 TRP 0.019 0.001 TRP A 204 HIS 0.004 0.001 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00334 (22976) covalent geometry : angle 0.50671 (31202) SS BOND : bond 0.00164 ( 8) SS BOND : angle 2.50100 ( 16) hydrogen bonds : bond 0.04850 ( 1776) hydrogen bonds : angle 4.40879 ( 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: 55 poor density : 288 time to evaluate : 0.799 Fit side-chains REVERT: D 23 CYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8447 (m) REVERT: G 125 LEU cc_start: 0.8282 (tp) cc_final: 0.8058 (tt) REVERT: H 157 ASP cc_start: 0.7207 (OUTLIER) cc_final: 0.6948 (t0) REVERT: J 3 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7471 (tt0) REVERT: J 156 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.6744 (tt0) REVERT: B 109 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8112 (tp) REVERT: B 145 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7286 (tp) REVERT: B 181 ARG cc_start: 0.7752 (tmm-80) cc_final: 0.7181 (ttm-80) REVERT: B 194 ASN cc_start: 0.7774 (m-40) cc_final: 0.7200 (m-40) REVERT: A 85 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6886 (mp0) REVERT: A 195 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7157 (mtpp) REVERT: A 746 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8534 (mp) outliers start: 55 outliers final: 32 residues processed: 322 average time/residue: 0.5440 time to fit residues: 204.1701 Evaluate side-chains 312 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 272 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 F residue 74 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 156 GLN 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 145 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 109 LEU 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 54 THR Chi-restraints excluded: chain A residue 85 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 62 optimal weight: 5.9990 chunk 258 optimal weight: 0.6980 chunk 117 optimal weight: 0.9980 chunk 229 optimal weight: 9.9990 chunk 116 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 212 optimal weight: 1.9990 chunk 157 optimal weight: 0.0050 chunk 234 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 151 ASN ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN A 499 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.154640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.120002 restraints weight = 21673.752| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.30 r_work: 0.3188 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22984 Z= 0.142 Angle : 0.505 9.951 31218 Z= 0.262 Chirality : 0.038 0.148 3711 Planarity : 0.004 0.042 3879 Dihedral : 8.145 112.113 3625 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.35 % Favored : 98.61 % Rotamer: Outliers : 1.75 % Allowed : 16.48 % Favored : 81.77 % 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: 2.11 (0.15), residues: 2881 helix: 1.85 (0.11), residues: 2187 sheet: -0.86 (0.80), 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 0.030 0.001 TYR L 66 PHE 0.024 0.001 PHE C 80 TRP 0.022 0.001 TRP A 204 HIS 0.004 0.000 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00311 (22976) covalent geometry : angle 0.50203 (31202) SS BOND : bond 0.00112 ( 8) SS BOND : angle 2.34153 ( 16) hydrogen bonds : bond 0.04765 ( 1776) hydrogen bonds : angle 4.37410 ( 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 321 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 280 time to evaluate : 0.595 Fit side-chains REVERT: D 23 CYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8421 (m) REVERT: C 86 MET cc_start: 0.8877 (mtp) cc_final: 0.8447 (ttm) REVERT: G 125 LEU cc_start: 0.8193 (tp) cc_final: 0.7968 (tt) REVERT: H 59 MET cc_start: 0.8668 (mmt) cc_final: 0.8282 (mmt) REVERT: H 157 ASP cc_start: 0.7173 (OUTLIER) cc_final: 0.6922 (t0) REVERT: B 109 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7978 (tp) REVERT: B 145 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7244 (tp) REVERT: B 181 ARG cc_start: 0.7707 (tmm-80) cc_final: 0.7048 (ttm-80) REVERT: B 194 ASN cc_start: 0.7716 (m-40) cc_final: 0.7139 (m-40) REVERT: A 85 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6906 (mp0) REVERT: A 124 MET cc_start: 0.7775 (mtt) cc_final: 0.7514 (mtm) REVERT: A 126 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7380 (p0) REVERT: A 195 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7113 (mtpp) REVERT: A 746 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8478 (mp) REVERT: A 753 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7561 (mmm) outliers start: 41 outliers final: 27 residues processed: 307 average time/residue: 0.5454 time to fit residues: 194.6735 Evaluate side-chains 310 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 274 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 131 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 145 ILE 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 109 LEU 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 85 GLU 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 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: 2.9990 chunk 259 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 268 optimal weight: 0.9990 chunk 196 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 200 optimal weight: 1.9990 chunk 190 optimal weight: 0.7980 chunk 226 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 275 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN A 499 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.153664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.118871 restraints weight = 21830.991| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.29 r_work: 0.3171 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 22984 Z= 0.156 Angle : 0.518 9.821 31218 Z= 0.268 Chirality : 0.039 0.179 3711 Planarity : 0.004 0.041 3879 Dihedral : 8.143 113.461 3625 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.35 % Favored : 98.61 % Rotamer: Outliers : 1.75 % Allowed : 16.44 % Favored : 81.81 % 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: 2186 sheet: -0.93 (0.80), residues: 38 loop : 0.10 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 352 TYR 0.035 0.001 TYR L 66 PHE 0.025 0.001 PHE C 80 TRP 0.028 0.001 TRP A 204 HIS 0.004 0.001 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00351 (22976) covalent geometry : angle 0.51514 (31202) SS BOND : bond 0.00149 ( 8) SS BOND : angle 2.50212 ( 16) hydrogen bonds : bond 0.04862 ( 1776) hydrogen bonds : angle 4.41409 ( 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 325 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 284 time to evaluate : 0.715 Fit side-chains REVERT: D 23 CYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8457 (m) REVERT: C 86 MET cc_start: 0.8903 (mtp) cc_final: 0.8487 (ttm) REVERT: G 125 LEU cc_start: 0.8233 (tp) cc_final: 0.8010 (tt) REVERT: H 157 ASP cc_start: 0.7157 (OUTLIER) cc_final: 0.6912 (t0) REVERT: J 3 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7584 (tt0) REVERT: L 46 ARG cc_start: 0.8597 (mmm-85) cc_final: 0.8198 (mtp180) REVERT: B 109 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8040 (tp) REVERT: B 145 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7270 (tp) REVERT: B 175 MET cc_start: 0.6351 (mmp) cc_final: 0.6108 (mmm) REVERT: B 181 ARG cc_start: 0.7752 (tmm-80) cc_final: 0.7171 (ttm-80) REVERT: B 194 ASN cc_start: 0.7780 (m-40) cc_final: 0.7216 (m-40) REVERT: B 274 GLU cc_start: 0.7711 (mp0) cc_final: 0.7445 (mp0) REVERT: A 85 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.6917 (mp0) REVERT: A 126 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7453 (p0) REVERT: A 195 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7186 (mtpp) REVERT: A 247 LYS cc_start: 0.8205 (tppt) cc_final: 0.8002 (tppp) REVERT: A 442 ASN cc_start: 0.7735 (m110) cc_final: 0.7110 (p0) REVERT: A 746 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8549 (mp) REVERT: A 753 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7679 (mmm) REVERT: A 762 ARG cc_start: 0.7090 (mmp80) cc_final: 0.6873 (mmp80) outliers start: 41 outliers final: 26 residues processed: 307 average time/residue: 0.5665 time to fit residues: 201.6618 Evaluate side-chains 317 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 282 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 F residue 74 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain L residue 145 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 109 LEU 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 85 GLU 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 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: 0.8980 chunk 133 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 246 optimal weight: 2.9990 chunk 224 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 237 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 266 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 156 GLN ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN A 499 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.153436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.118588 restraints weight = 21750.218| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.30 r_work: 0.3150 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22984 Z= 0.158 Angle : 0.523 11.735 31218 Z= 0.269 Chirality : 0.039 0.166 3711 Planarity : 0.004 0.042 3879 Dihedral : 8.131 113.859 3625 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 : 2.13 % Allowed : 16.23 % Favored : 81.64 % 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: 2.05 (0.15), residues: 2881 helix: 1.81 (0.11), residues: 2187 sheet: -0.97 (0.80), residues: 38 loop : 0.11 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 352 TYR 0.037 0.001 TYR L 66 PHE 0.026 0.001 PHE C 80 TRP 0.032 0.001 TRP A 204 HIS 0.004 0.001 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00357 (22976) covalent geometry : angle 0.51992 (31202) SS BOND : bond 0.00148 ( 8) SS BOND : angle 2.47968 ( 16) hydrogen bonds : bond 0.04872 ( 1776) hydrogen bonds : angle 4.42835 ( 5208) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6958.48 seconds wall clock time: 119 minutes 24.40 seconds (7164.40 seconds total)