Starting phenix.real_space_refine on Thu Aug 8 08:44:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tap_25780/08_2024/7tap_25780.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tap_25780/08_2024/7tap_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tap_25780/08_2024/7tap_25780.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tap_25780/08_2024/7tap_25780.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tap_25780/08_2024/7tap_25780.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tap_25780/08_2024/7tap_25780.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 Residue "D TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 89": "OD1" <-> "OD2" Residue "C PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "N ASP 248": "OD1" <-> "OD2" Residue "M GLU 70": "OE1" <-> "OE2" Residue "E TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 47": "OD1" <-> "OD2" Residue "F TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 137": "OE1" <-> "OE2" Residue "H TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 137": "OE1" <-> "OE2" Residue "K TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 105": "OD1" <-> "OD2" Residue "B GLU 263": "OE1" <-> "OE2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "A TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 818": "OE1" <-> "OE2" Residue "A TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/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: 11.77, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 9.11 Conformation dependent library (CDL) restraints added in 3.7 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: 1.75 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: 7.52 Time building geometry restraints manager: 9.95 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: 96.55 - 104.12: 269 104.12 - 111.69: 10451 111.69 - 119.27: 8589 119.27 - 126.84: 11665 126.84 - 134.41: 228 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: 0.010 Normalize map: mean=0, sd=1: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 58.580 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.100 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:12.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.660 ------------------------------------------------------------------------------- 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 22976 Z= 0.827 Angle : 1.473 14.522 31202 Z= 1.031 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 : 8.19 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (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 TRP 0.029 0.002 TRP B 312 HIS 0.009 0.001 HIS A 801 PHE 0.029 0.002 PHE L 23 TYR 0.026 0.002 TYR F 66 ARG 0.007 0.001 ARG K 153 *********************** 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 fitting. rotamer outliers: 32 poor density : 328 time to evaluate : 2.418 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: 0.8757 (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: 0.8376 (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: 1.1036 time to fit residues: 451.7451 Evaluate side-chains 268 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 260 time to evaluate : 2.165 ------------------------------------------------------------------------------- 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 237 optimal weight: 2.9990 chunk 212 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 72 optimal weight: 0.0030 chunk 143 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 220 optimal weight: 8.9990 chunk 85 optimal weight: 0.6980 chunk 133 optimal weight: 0.9980 chunk 163 optimal weight: 0.8980 chunk 255 optimal weight: 0.9980 overall best weight: 0.5990 ------------------------------------------------------------------------------- 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** I 80 GLN K 82 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN A 210 ASN A 442 ASN A 499 HIS ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 634 GLN A 796 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22976 Z= 0.224 Angle : 0.566 6.432 31202 Z= 0.299 Chirality : 0.040 0.151 3711 Planarity : 0.004 0.058 3879 Dihedral : 10.014 120.821 3645 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.04 % Favored : 98.92 % Rotamer: Outliers : 2.26 % Allowed : 8.84 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.15), residues: 2881 helix: 1.65 (0.11), residues: 2143 sheet: -0.60 (0.76), residues: 42 loop : 0.02 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 737 HIS 0.003 0.001 HIS A 801 PHE 0.029 0.002 PHE C 80 TYR 0.018 0.001 TYR D 127 ARG 0.007 0.000 ARG A 205 *********************** 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 357 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 304 time to evaluate : 2.332 Fit side-chains REVERT: D 94 ASN cc_start: 0.8297 (t0) cc_final: 0.8019 (t160) REVERT: C 106 PHE cc_start: 0.8772 (m-10) cc_final: 0.8568 (m-80) REVERT: C 134 TYR cc_start: 0.8992 (m-80) cc_final: 0.8643 (m-80) REVERT: G 8 TYR cc_start: 0.8704 (p90) cc_final: 0.8471 (p90) REVERT: J 59 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7880 (mmm) REVERT: K 138 VAL cc_start: 0.8111 (OUTLIER) cc_final: 0.7880 (p) REVERT: B 178 GLU cc_start: 0.7015 (tp30) cc_final: 0.6201 (tt0) REVERT: B 185 TYR cc_start: 0.7885 (OUTLIER) cc_final: 0.7608 (m-80) REVERT: B 194 ASN cc_start: 0.7303 (m-40) cc_final: 0.6744 (m-40) REVERT: B 254 PHE cc_start: 0.7807 (t80) cc_final: 0.7592 (t80) REVERT: B 258 GLN cc_start: 0.7697 (mp10) cc_final: 0.7273 (mt0) REVERT: B 313 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7591 (tpt) REVERT: B 334 GLN cc_start: 0.7665 (mp10) cc_final: 0.7398 (mt0) REVERT: A 195 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.6824 (mtpp) REVERT: A 746 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8414 (mp) REVERT: A 761 PHE cc_start: 0.7519 (m-10) cc_final: 0.7230 (m-10) REVERT: A 762 ARG cc_start: 0.7484 (mmt-90) cc_final: 0.6948 (mmp80) REVERT: A 804 GLU cc_start: 0.8227 (mp0) cc_final: 0.7873 (mp0) outliers start: 53 outliers final: 13 residues processed: 339 average time/residue: 1.1433 time to fit residues: 452.6774 Evaluate side-chains 280 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 261 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain J residue 59 MET 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 B residue 34 THR Chi-restraints excluded: chain B residue 138 THR 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 141 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 212 optimal weight: 3.9990 chunk 173 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 255 optimal weight: 0.0170 chunk 276 optimal weight: 0.9990 chunk 227 optimal weight: 0.9980 chunk 253 optimal weight: 7.9990 chunk 87 optimal weight: 0.0980 chunk 205 optimal weight: 0.7980 overall best weight: 0.4218 ------------------------------------------------------------------------------- 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** ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN K 151 ASN L 151 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN A 201 GLN A 210 ASN A 442 ASN A 499 HIS A 533 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 22976 Z= 0.184 Angle : 0.497 7.972 31202 Z= 0.263 Chirality : 0.038 0.181 3711 Planarity : 0.004 0.047 3879 Dihedral : 9.250 113.119 3631 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.15 % Favored : 98.82 % Rotamer: Outliers : 2.43 % Allowed : 11.74 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.15), residues: 2881 helix: 1.90 (0.11), residues: 2157 sheet: -0.49 (0.73), residues: 44 loop : 0.11 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 737 HIS 0.003 0.000 HIS A 801 PHE 0.025 0.001 PHE C 80 TYR 0.022 0.001 TYR A 99 ARG 0.006 0.000 ARG A 205 *********************** 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 339 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 282 time to evaluate : 2.330 Fit side-chains REVERT: D 23 CYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7955 (m) REVERT: D 94 ASN cc_start: 0.8245 (t0) cc_final: 0.7967 (t160) REVERT: C 108 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8359 (tt0) REVERT: C 134 TYR cc_start: 0.8936 (m-80) cc_final: 0.8606 (m-80) REVERT: E 81 LYS cc_start: 0.8831 (mttm) cc_final: 0.8609 (mttm) REVERT: G 50 LEU cc_start: 0.8197 (tp) cc_final: 0.7984 (tt) REVERT: G 52 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7694 (pttm) REVERT: K 82 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8264 (pt0) REVERT: B 145 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7343 (tp) REVERT: B 175 MET cc_start: 0.6108 (mmm) cc_final: 0.5855 (mpp) REVERT: B 181 ARG cc_start: 0.7303 (tmm-80) cc_final: 0.6767 (ttp-110) REVERT: B 194 ASN cc_start: 0.7411 (m-40) cc_final: 0.6864 (m-40) REVERT: B 254 PHE cc_start: 0.7856 (t80) cc_final: 0.7613 (t80) REVERT: B 258 GLN cc_start: 0.7747 (mp10) cc_final: 0.7145 (mt0) REVERT: B 297 ARG cc_start: 0.7842 (ttp-170) cc_final: 0.7604 (ttm110) REVERT: B 313 MET cc_start: 0.7879 (mmm) cc_final: 0.7513 (tpt) REVERT: A 23 GLN cc_start: 0.7237 (OUTLIER) cc_final: 0.6834 (tt0) REVERT: A 195 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.6821 (mtpp) REVERT: A 746 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8399 (mp) REVERT: A 761 PHE cc_start: 0.7442 (m-10) cc_final: 0.7216 (m-10) REVERT: A 762 ARG cc_start: 0.7514 (mmt-90) cc_final: 0.6936 (mmp80) outliers start: 57 outliers final: 14 residues processed: 318 average time/residue: 1.1545 time to fit residues: 427.3825 Evaluate side-chains 281 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 259 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain C residue 108 GLU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 510 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 252 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 132 optimal weight: 0.4980 chunk 28 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 171 optimal weight: 0.6980 chunk 256 optimal weight: 0.7980 chunk 271 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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** 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** J 82 GLN K 82 GLN B 244 ASN A 210 ASN A 442 ASN A 499 HIS A 533 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 22976 Z= 0.250 Angle : 0.515 7.902 31202 Z= 0.269 Chirality : 0.039 0.166 3711 Planarity : 0.004 0.044 3879 Dihedral : 8.976 112.747 3625 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.39 % Favored : 98.58 % Rotamer: Outliers : 2.60 % Allowed : 12.51 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.15), residues: 2881 helix: 1.91 (0.11), residues: 2152 sheet: -0.65 (0.75), residues: 42 loop : 0.00 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 737 HIS 0.005 0.001 HIS A 801 PHE 0.026 0.002 PHE C 80 TYR 0.022 0.001 TYR A 99 ARG 0.006 0.000 ARG K 153 *********************** 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 339 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 278 time to evaluate : 2.310 Fit side-chains REVERT: D 23 CYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8045 (m) REVERT: D 94 ASN cc_start: 0.8246 (t0) cc_final: 0.7953 (t160) REVERT: C 108 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8384 (tt0) REVERT: C 134 TYR cc_start: 0.9013 (m-80) cc_final: 0.8744 (m-80) REVERT: H 99 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8259 (mm) REVERT: J 3 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6903 (tm-30) REVERT: K 82 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8609 (pt0) REVERT: K 124 ARG cc_start: 0.8665 (mtp180) cc_final: 0.8375 (mtp180) REVERT: B 109 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7811 (tp) REVERT: B 145 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7436 (tp) REVERT: B 175 MET cc_start: 0.6190 (mmm) cc_final: 0.5917 (mpp) REVERT: B 194 ASN cc_start: 0.7409 (m-40) cc_final: 0.6846 (m-40) REVERT: B 313 MET cc_start: 0.7871 (mmm) cc_final: 0.7565 (tpt) REVERT: A 23 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.6993 (tt0) REVERT: A 195 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.6861 (mtpp) REVERT: A 746 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8453 (mp) REVERT: A 762 ARG cc_start: 0.7528 (mmt-90) cc_final: 0.6868 (mmp80) outliers start: 61 outliers final: 22 residues processed: 311 average time/residue: 1.1883 time to fit residues: 431.0230 Evaluate side-chains 292 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 260 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 108 GLU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 3 GLU Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain L residue 62 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 4 LYS Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 432 MET 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 746 LEU Chi-restraints excluded: chain A residue 753 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 226 optimal weight: 0.7980 chunk 154 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 112 optimal weight: 0.5980 chunk 231 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 C 100 ASN E 53 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** K 82 GLN B 244 ASN A 210 ASN A 442 ASN A 499 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22976 Z= 0.283 Angle : 0.530 10.869 31202 Z= 0.275 Chirality : 0.040 0.179 3711 Planarity : 0.004 0.045 3879 Dihedral : 8.836 113.214 3625 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.46 % Favored : 98.51 % Rotamer: Outliers : 2.52 % Allowed : 13.62 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.15), residues: 2881 helix: 1.82 (0.11), residues: 2144 sheet: -0.53 (0.80), residues: 36 loop : -0.08 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 737 HIS 0.005 0.001 HIS A 801 PHE 0.027 0.002 PHE C 80 TYR 0.024 0.001 TYR A 99 ARG 0.007 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 282 time to evaluate : 2.567 Fit side-chains REVERT: D 23 CYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8087 (m) REVERT: C 86 MET cc_start: 0.8522 (mtp) cc_final: 0.8044 (ttm) REVERT: C 108 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8335 (tt0) REVERT: C 134 TYR cc_start: 0.9040 (m-80) cc_final: 0.8792 (m-80) REVERT: G 82 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8412 (pp30) REVERT: H 59 MET cc_start: 0.8487 (mtp) cc_final: 0.7944 (mmt) REVERT: J 3 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6999 (tt0) REVERT: B 109 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7987 (tp) REVERT: B 145 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7522 (tp) REVERT: B 175 MET cc_start: 0.6170 (mmm) cc_final: 0.5904 (mpp) REVERT: B 181 ARG cc_start: 0.7543 (tmm-80) cc_final: 0.6878 (ttm170) REVERT: B 194 ASN cc_start: 0.7463 (m-40) cc_final: 0.6854 (m-40) REVERT: B 313 MET cc_start: 0.7919 (mmm) cc_final: 0.7572 (tpt) REVERT: A 85 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7097 (mp0) REVERT: A 195 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.6889 (mtpp) REVERT: A 369 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7506 (tm-30) REVERT: A 746 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8505 (mp) REVERT: A 762 ARG cc_start: 0.7520 (mmt-90) cc_final: 0.6835 (mmp80) outliers start: 59 outliers final: 25 residues processed: 318 average time/residue: 1.1656 time to fit residues: 433.3659 Evaluate side-chains 299 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 264 time to evaluate : 2.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 108 GLU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain I residue 7 VAL 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 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 4 LYS Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 85 GLU 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 369 GLN 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 746 LEU Chi-restraints excluded: chain A residue 753 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 91 optimal weight: 1.9990 chunk 244 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 159 optimal weight: 2.9990 chunk 67 optimal weight: 0.0970 chunk 271 optimal weight: 0.7980 chunk 225 optimal weight: 10.0000 chunk 125 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN O 72 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 B 244 ASN A 210 ASN A 442 ASN A 499 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22976 Z= 0.189 Angle : 0.490 11.328 31202 Z= 0.256 Chirality : 0.038 0.148 3711 Planarity : 0.004 0.044 3879 Dihedral : 8.429 110.506 3625 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.28 % Favored : 98.68 % Rotamer: Outliers : 2.39 % Allowed : 14.73 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.15), residues: 2881 helix: 1.84 (0.11), residues: 2187 sheet: -0.72 (0.79), residues: 38 loop : 0.11 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 204 HIS 0.003 0.000 HIS A 801 PHE 0.023 0.001 PHE C 80 TYR 0.025 0.001 TYR A 99 ARG 0.008 0.000 ARG K 153 *********************** 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 343 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 287 time to evaluate : 2.323 Fit side-chains REVERT: D 23 CYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8032 (m) REVERT: C 108 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8389 (tt0) REVERT: C 134 TYR cc_start: 0.8987 (m-80) cc_final: 0.8657 (m-80) REVERT: B 109 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7875 (tp) REVERT: B 145 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7500 (tp) REVERT: B 178 GLU cc_start: 0.7151 (tp30) cc_final: 0.6303 (tt0) REVERT: B 181 ARG cc_start: 0.7527 (tmm-80) cc_final: 0.7149 (ttp-110) REVERT: B 194 ASN cc_start: 0.7420 (m-40) cc_final: 0.6836 (m-40) REVERT: B 313 MET cc_start: 0.7900 (mmm) cc_final: 0.7562 (tpt) REVERT: A 195 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.6876 (mtpp) REVERT: A 369 GLN cc_start: 0.7677 (tm-30) cc_final: 0.7473 (tm-30) REVERT: A 499 HIS cc_start: 0.6848 (t70) cc_final: 0.6370 (t-90) REVERT: A 746 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8444 (mp) REVERT: A 762 ARG cc_start: 0.7465 (mmt-90) cc_final: 0.6900 (mmp80) outliers start: 56 outliers final: 24 residues processed: 318 average time/residue: 1.1460 time to fit residues: 431.5411 Evaluate side-chains 302 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 272 time to evaluate : 2.310 ------------------------------------------------------------------------------- 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 108 GLU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 129 MET Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 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 344 ASP Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 746 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 262 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 228 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 270 optimal weight: 0.9990 chunk 169 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** K 82 GLN ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN A 210 ASN A 442 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 22976 Z= 0.296 Angle : 0.540 9.866 31202 Z= 0.280 Chirality : 0.040 0.192 3711 Planarity : 0.004 0.044 3879 Dihedral : 8.462 113.951 3625 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.56 % Favored : 98.40 % Rotamer: Outliers : 2.52 % Allowed : 15.20 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.15), residues: 2881 helix: 1.68 (0.11), residues: 2187 sheet: -0.79 (0.80), residues: 38 loop : 0.04 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 204 HIS 0.006 0.001 HIS A 801 PHE 0.031 0.002 PHE A 774 TYR 0.030 0.002 TYR L 66 ARG 0.006 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 287 time to evaluate : 2.359 Fit side-chains REVERT: D 23 CYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8098 (m) REVERT: C 86 MET cc_start: 0.8594 (mtp) cc_final: 0.8235 (ttm) REVERT: C 108 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8238 (tt0) REVERT: H 157 ASP cc_start: 0.6775 (OUTLIER) cc_final: 0.6505 (t0) REVERT: J 156 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.6676 (tt0) REVERT: B 109 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8044 (tp) REVERT: B 145 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7516 (tp) REVERT: B 181 ARG cc_start: 0.7597 (tmm-80) cc_final: 0.7056 (ttm-80) REVERT: B 194 ASN cc_start: 0.7469 (m-40) cc_final: 0.6856 (m-40) REVERT: A 85 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7061 (mp0) REVERT: A 195 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.6988 (mtpp) REVERT: A 369 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7371 (tm-30) REVERT: A 746 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8509 (mp) REVERT: A 762 ARG cc_start: 0.7513 (mmt-90) cc_final: 0.6914 (mmp80) outliers start: 59 outliers final: 29 residues processed: 320 average time/residue: 1.1079 time to fit residues: 416.0150 Evaluate side-chains 314 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 275 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 108 GLU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 129 MET Chi-restraints excluded: chain J residue 156 GLN Chi-restraints excluded: chain K residue 131 LEU 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 46 SER Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 369 GLN 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 776 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 167 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 172 optimal weight: 0.9990 chunk 184 optimal weight: 0.5980 chunk 133 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 212 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN A 210 ASN A 499 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 22976 Z= 0.217 Angle : 0.511 11.348 31202 Z= 0.265 Chirality : 0.038 0.150 3711 Planarity : 0.004 0.044 3879 Dihedral : 8.275 112.475 3625 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.32 % Favored : 98.65 % Rotamer: Outliers : 2.09 % Allowed : 15.88 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.15), residues: 2881 helix: 1.77 (0.11), residues: 2187 sheet: -0.88 (0.79), residues: 38 loop : 0.08 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 204 HIS 0.004 0.001 HIS A 801 PHE 0.025 0.001 PHE C 80 TYR 0.026 0.001 TYR L 66 ARG 0.006 0.000 ARG A 205 *********************** 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 331 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 282 time to evaluate : 2.745 Fit side-chains REVERT: D 23 CYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8049 (m) REVERT: C 86 MET cc_start: 0.8530 (mtp) cc_final: 0.8132 (ttm) REVERT: C 108 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8396 (tt0) REVERT: C 134 TYR cc_start: 0.9030 (m-80) cc_final: 0.8762 (m-80) REVERT: F 119 SER cc_start: 0.8334 (m) cc_final: 0.8117 (m) REVERT: J 3 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7123 (tt0) REVERT: J 156 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.6695 (tt0) REVERT: B 109 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7837 (tp) REVERT: B 145 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7543 (tp) REVERT: B 181 ARG cc_start: 0.7575 (tmm-80) cc_final: 0.6958 (ttm-80) REVERT: B 194 ASN cc_start: 0.7462 (m-40) cc_final: 0.6863 (m-40) REVERT: A 195 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.6921 (mtpp) REVERT: A 369 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.7351 (tm-30) REVERT: A 746 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8491 (mp) REVERT: A 762 ARG cc_start: 0.7505 (mmt-90) cc_final: 0.6843 (mmp80) outliers start: 49 outliers final: 27 residues processed: 311 average time/residue: 1.1293 time to fit residues: 411.5796 Evaluate side-chains 311 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 275 time to evaluate : 2.436 ------------------------------------------------------------------------------- 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 108 GLU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 3 GLU Chi-restraints excluded: chain J residue 129 MET 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 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 369 GLN 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 246 optimal weight: 0.8980 chunk 259 optimal weight: 4.9990 chunk 236 optimal weight: 7.9990 chunk 252 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 228 optimal weight: 0.0980 chunk 238 optimal weight: 5.9990 chunk 251 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 ASN F 151 ASN ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 GLN ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN A 210 ASN A 499 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 : 0.004 0.068 22976 Z= 0.278 Angle : 0.543 10.699 31202 Z= 0.279 Chirality : 0.040 0.181 3711 Planarity : 0.004 0.043 3879 Dihedral : 8.325 114.356 3625 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.56 % Favored : 98.40 % Rotamer: Outliers : 2.09 % Allowed : 16.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.15), residues: 2881 helix: 1.69 (0.11), residues: 2187 sheet: -0.73 (0.82), residues: 36 loop : 0.07 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 204 HIS 0.006 0.001 HIS A 801 PHE 0.027 0.002 PHE C 80 TYR 0.034 0.001 TYR L 66 ARG 0.007 0.000 ARG A 205 *********************** 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 335 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 286 time to evaluate : 2.302 Fit side-chains REVERT: D 23 CYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8088 (m) REVERT: C 86 MET cc_start: 0.8570 (mtp) cc_final: 0.8194 (ttm) REVERT: C 108 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8229 (tt0) REVERT: F 119 SER cc_start: 0.8349 (m) cc_final: 0.8108 (m) REVERT: H 157 ASP cc_start: 0.6674 (OUTLIER) cc_final: 0.6424 (t0) REVERT: B 109 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7901 (tp) REVERT: B 145 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7561 (tp) REVERT: B 181 ARG cc_start: 0.7588 (tmm-80) cc_final: 0.6972 (ttm-80) REVERT: B 194 ASN cc_start: 0.7478 (m-40) cc_final: 0.6866 (m-40) REVERT: A 23 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.7067 (tt0) REVERT: A 195 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7010 (mtpp) REVERT: A 247 LYS cc_start: 0.8167 (tppt) cc_final: 0.7966 (tppp) REVERT: A 369 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.7320 (tm-30) REVERT: A 746 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8521 (mp) REVERT: A 753 MET cc_start: 0.7484 (mtt) cc_final: 0.7235 (mmm) REVERT: A 762 ARG cc_start: 0.7505 (mmt-90) cc_final: 0.6843 (mmp80) outliers start: 49 outliers final: 29 residues processed: 315 average time/residue: 1.1595 time to fit residues: 427.9786 Evaluate side-chains 314 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 276 time to evaluate : 2.628 ------------------------------------------------------------------------------- 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 108 GLU 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 131 LEU Chi-restraints excluded: chain J residue 129 MET Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 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 23 GLN Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 54 THR 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 369 GLN 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 776 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.8033 > 50: distance: 45 - 62: 7.087 distance: 49 - 70: 8.683 distance: 54 - 58: 5.414 distance: 55 - 82: 15.700 distance: 58 - 59: 4.180 distance: 60 - 61: 8.090 distance: 60 - 62: 3.143 distance: 61 - 86: 14.202 distance: 63 - 64: 4.369 distance: 63 - 66: 7.380 distance: 64 - 65: 5.346 distance: 64 - 70: 6.928 distance: 65 - 94: 9.893 distance: 66 - 67: 3.987 distance: 67 - 69: 5.103 distance: 71 - 72: 5.286 distance: 72 - 73: 8.005 distance: 72 - 82: 7.623 distance: 73 - 102: 16.479 distance: 74 - 75: 6.013 distance: 75 - 76: 3.968 distance: 75 - 77: 8.530 distance: 77 - 79: 4.542 distance: 78 - 80: 4.092 distance: 79 - 80: 5.820 distance: 82 - 83: 5.936 distance: 83 - 84: 10.261 distance: 84 - 85: 4.494 distance: 84 - 86: 5.557 distance: 85 - 109: 26.393 distance: 86 - 87: 12.828 distance: 87 - 88: 10.865 distance: 87 - 90: 12.600 distance: 88 - 89: 5.072 distance: 88 - 94: 6.342 distance: 89 - 114: 40.046 distance: 90 - 91: 5.802 distance: 91 - 92: 6.155 distance: 91 - 93: 17.344 distance: 94 - 95: 9.366 distance: 95 - 96: 6.649 distance: 95 - 98: 7.742 distance: 96 - 97: 9.793 distance: 96 - 102: 12.761 distance: 97 - 122: 5.616 distance: 98 - 99: 7.258 distance: 98 - 100: 12.074 distance: 99 - 101: 4.046 distance: 102 - 103: 3.638 distance: 103 - 104: 16.155 distance: 103 - 106: 9.154 distance: 104 - 105: 28.048 distance: 104 - 109: 27.625 distance: 105 - 130: 23.126 distance: 106 - 107: 5.327 distance: 106 - 108: 10.209 distance: 109 - 110: 48.661 distance: 110 - 111: 11.538 distance: 110 - 113: 16.717 distance: 111 - 112: 9.672 distance: 111 - 114: 15.568 distance: 112 - 137: 25.887 distance: 114 - 115: 12.708 distance: 115 - 116: 8.550 distance: 115 - 118: 9.676 distance: 116 - 122: 3.693 distance: 118 - 119: 5.071 distance: 119 - 120: 11.657 distance: 119 - 121: 7.295 distance: 123 - 124: 4.389 distance: 123 - 126: 3.986 distance: 124 - 125: 4.128 distance: 124 - 130: 3.201 distance: 126 - 127: 5.105 distance: 127 - 128: 4.726 distance: 127 - 129: 3.280