Starting phenix.real_space_refine on Thu Jun 19 13:47:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tap_25780/06_2025/7tap_25780.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tap_25780/06_2025/7tap_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/cci-nas-00/data/ceres_data/7tap_25780/06_2025/7tap_25780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tap_25780/06_2025/7tap_25780.map" model { file = "/net/cci-nas-00/data/ceres_data/7tap_25780/06_2025/7tap_25780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tap_25780/06_2025/7tap_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. Time to flip 35 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 13.57, per 1000 atoms: 0.60 Number of scatterers: 22520 At special positions: 0 Unit cell: (123.6, 121.54, 133.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 143 16.00 O 3998 8.00 N 3558 7.00 C 14821 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 17 " - pdb=" SG CYS E 75 " distance=2.08 Simple disulfide: pdb=" SG CYS F 17 " - pdb=" SG CYS F 75 " distance=2.05 Simple disulfide: pdb=" SG CYS G 17 " - pdb=" SG CYS G 75 " distance=2.06 Simple disulfide: pdb=" SG CYS H 17 " - pdb=" SG CYS H 75 " distance=2.07 Simple disulfide: pdb=" SG CYS I 17 " - pdb=" SG CYS I 75 " distance=2.05 Simple disulfide: pdb=" SG CYS J 17 " - pdb=" SG CYS J 75 " distance=2.07 Simple disulfide: pdb=" SG CYS K 17 " - pdb=" SG CYS K 75 " distance=2.05 Simple disulfide: pdb=" SG CYS L 17 " - pdb=" SG CYS L 75 " distance=2.10 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.32 Conformation dependent library (CDL) restraints added in 3.0 seconds 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5252 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 7 sheets defined 79.7% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.03 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: 7.97 Time building geometry restraints manager: 7.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 3501 1.27 - 1.41: 5746 1.41 - 1.55: 13358 1.55 - 1.69: 167 1.69 - 1.82: 204 Bond restraints: 22976 Sorted by residual: bond pdb=" C SER G 96 " pdb=" O SER G 96 " ideal model delta sigma weight residual 1.236 1.135 0.101 1.16e-02 7.43e+03 7.62e+01 bond pdb=" C LEU I 141 " pdb=" O LEU I 141 " ideal model delta sigma weight residual 1.237 1.135 0.102 1.17e-02 7.31e+03 7.54e+01 bond pdb=" C ILE G 134 " pdb=" O ILE G 134 " ideal model delta sigma weight residual 1.237 1.141 0.097 1.17e-02 7.31e+03 6.83e+01 bond pdb=" C ILE K 134 " pdb=" O ILE K 134 " ideal model delta sigma weight residual 1.237 1.140 0.096 1.19e-02 7.06e+03 6.57e+01 bond pdb=" C ILE E 134 " pdb=" O ILE E 134 " ideal model delta sigma weight residual 1.237 1.142 0.095 1.19e-02 7.06e+03 6.38e+01 ... (remaining 22971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 28771 2.90 - 5.81: 2185 5.81 - 8.71: 207 8.71 - 11.62: 37 11.62 - 14.52: 2 Bond angle restraints: 31202 Sorted by residual: angle pdb=" CA ALA F 20 " pdb=" C ALA F 20 " pdb=" O ALA F 20 " ideal model delta sigma weight residual 120.82 112.05 8.77 1.05e+00 9.07e-01 6.98e+01 angle pdb=" CA ALA H 20 " pdb=" C ALA H 20 " pdb=" O ALA H 20 " ideal model delta sigma weight residual 120.82 112.49 8.33 1.05e+00 9.07e-01 6.30e+01 angle pdb=" CA ALA E 20 " pdb=" C ALA E 20 " pdb=" O ALA E 20 " ideal model delta sigma weight residual 120.82 112.68 8.14 1.05e+00 9.07e-01 6.01e+01 angle pdb=" N LEU L 68 " pdb=" CA LEU L 68 " pdb=" C LEU L 68 " ideal model delta sigma weight residual 112.23 102.59 9.64 1.26e+00 6.30e-01 5.86e+01 angle pdb=" CA GLU G 137 " pdb=" C GLU G 137 " pdb=" N VAL G 138 " ideal model delta sigma weight residual 117.30 125.78 -8.48 1.16e+00 7.43e-01 5.34e+01 ... (remaining 31197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.54: 12878 24.54 - 49.07: 608 49.07 - 73.61: 118 73.61 - 98.14: 38 98.14 - 122.68: 4 Dihedral angle restraints: 13646 sinusoidal: 5372 harmonic: 8274 Sorted by residual: dihedral pdb=" CB CYS I 17 " pdb=" SG CYS I 17 " pdb=" SG CYS I 75 " pdb=" CB CYS I 75 " ideal model delta sinusoidal sigma weight residual -86.00 -167.40 81.40 1 1.00e+01 1.00e-02 8.16e+01 dihedral pdb=" CB CYS E 17 " pdb=" SG CYS E 17 " pdb=" SG CYS E 75 " pdb=" CB CYS E 75 " ideal model delta sinusoidal sigma weight residual -86.00 -165.14 79.14 1 1.00e+01 1.00e-02 7.79e+01 dihedral pdb=" CB CYS G 17 " pdb=" SG CYS G 17 " pdb=" SG CYS G 75 " pdb=" CB CYS G 75 " ideal model delta sinusoidal sigma weight residual -86.00 -129.63 43.63 1 1.00e+01 1.00e-02 2.65e+01 ... (remaining 13643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2950 0.074 - 0.148: 570 0.148 - 0.223: 145 0.223 - 0.297: 28 0.297 - 0.371: 18 Chirality restraints: 3711 Sorted by residual: chirality pdb=" CB THR I 24 " pdb=" CA THR I 24 " pdb=" OG1 THR I 24 " pdb=" CG2 THR I 24 " both_signs ideal model delta sigma weight residual False 2.55 2.18 0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" C09 KJL F 201 " pdb=" C08 KJL F 201 " pdb=" C10 KJL F 201 " pdb=" O48 KJL F 201 " both_signs ideal model delta sigma weight residual False -2.38 -2.74 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" C09 KJL E 201 " pdb=" C08 KJL E 201 " pdb=" C10 KJL E 201 " pdb=" O48 KJL E 201 " both_signs ideal model delta sigma weight residual False -2.38 -2.74 0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 3708 not shown) Planarity restraints: 3879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY G 67 " 0.025 2.00e-02 2.50e+03 5.18e-02 2.68e+01 pdb=" C GLY G 67 " -0.090 2.00e-02 2.50e+03 pdb=" O GLY G 67 " 0.033 2.00e-02 2.50e+03 pdb=" N LEU G 68 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY K 67 " -0.025 2.00e-02 2.50e+03 5.10e-02 2.60e+01 pdb=" C GLY K 67 " 0.088 2.00e-02 2.50e+03 pdb=" O GLY K 67 " -0.033 2.00e-02 2.50e+03 pdb=" N LEU K 68 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER L 71 " -0.023 2.00e-02 2.50e+03 4.88e-02 2.38e+01 pdb=" C SER L 71 " 0.084 2.00e-02 2.50e+03 pdb=" O SER L 71 " -0.032 2.00e-02 2.50e+03 pdb=" N VAL L 72 " -0.029 2.00e-02 2.50e+03 ... (remaining 3876 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3468 2.76 - 3.30: 24187 3.30 - 3.83: 40448 3.83 - 4.37: 52195 4.37 - 4.90: 85086 Nonbonded interactions: 205384 Sorted by model distance: nonbonded pdb=" OG SER B 315 " pdb=" OH TYR B 345 " model vdw 2.225 3.040 nonbonded pdb=" OH TYR A 116 " pdb=" NH1 ARG A 120 " model vdw 2.238 3.120 nonbonded pdb=" O LEU A 38 " pdb=" OH TYR A 817 " model vdw 2.240 3.040 nonbonded pdb=" O LEU N 254 " pdb=" NE2 GLN K 121 " model vdw 2.250 3.120 nonbonded pdb=" O ASP A 224 " pdb=" N ARG A 228 " model vdw 2.251 3.120 ... (remaining 205379 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'E' and resid 1 through 159) selection = (chain 'F' and resid 1 through 159) selection = (chain 'G' and resid 1 through 159) selection = (chain 'H' and resid 1 through 159) selection = (chain 'I' and resid 1 through 159) selection = (chain 'J' and resid 1 through 159) selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.760 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: 0.900 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 52.810 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.110 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:14.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.134 22984 Z= 0.847 Angle : 1.487 18.114 31218 Z= 1.035 Chirality : 0.069 0.371 3711 Planarity : 0.008 0.084 3879 Dihedral : 15.279 122.681 8370 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.19 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 Details of bonding type rmsd hydrogen bonds : bond 0.18438 ( 1776) hydrogen bonds : angle 7.73298 ( 5208) SS BOND : bond 0.03939 ( 8) SS BOND : angle 9.06549 ( 16) covalent geometry : bond 0.01269 (22976) covalent geometry : angle 1.47335 (31202) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 328 time to evaluate : 2.487 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: 1.1621 time to fit residues: 474.3875 Evaluate side-chains 268 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 260 time to evaluate : 2.466 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.151619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.114806 restraints weight = 21152.507| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.34 r_work: 0.3154 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 22984 Z= 0.163 Angle : 0.567 6.432 31218 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 Details of bonding type rmsd hydrogen bonds : bond 0.05275 ( 1776) hydrogen bonds : angle 4.56552 ( 5208) SS BOND : bond 0.00387 ( 8) SS BOND : angle 1.75313 ( 16) covalent geometry : bond 0.00346 (22976) covalent geometry : angle 0.56615 (31202) *********************** 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 to be fit. rotamer outliers: 53 poor density : 304 time to evaluate : 2.279 Fit side-chains REVERT: D 94 ASN cc_start: 0.8608 (t0) cc_final: 0.8396 (t160) REVERT: C 134 TYR cc_start: 0.9050 (m-80) cc_final: 0.8715 (m-80) REVERT: G 8 TYR cc_start: 0.8882 (p90) cc_final: 0.8637 (p90) REVERT: J 59 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8314 (mmm) REVERT: K 138 VAL cc_start: 0.8204 (OUTLIER) cc_final: 0.7969 (p) REVERT: B 178 GLU cc_start: 0.7074 (tp30) cc_final: 0.6002 (tt0) REVERT: B 185 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.7952 (m-80) REVERT: B 194 ASN cc_start: 0.7608 (m-40) cc_final: 0.7051 (m-40) REVERT: B 258 GLN cc_start: 0.7445 (mp10) cc_final: 0.6956 (mt0) REVERT: B 313 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8348 (tpt) REVERT: B 334 GLN cc_start: 0.7646 (mp10) cc_final: 0.7271 (mt0) REVERT: A 195 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.6922 (mtpp) REVERT: A 746 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8353 (mp) REVERT: A 761 PHE cc_start: 0.7520 (m-10) cc_final: 0.7044 (m-10) REVERT: A 762 ARG cc_start: 0.7421 (mmt-90) cc_final: 0.6528 (mmp80) REVERT: A 804 GLU cc_start: 0.8501 (mp0) cc_final: 0.8174 (mp0) outliers start: 53 outliers final: 13 residues processed: 339 average time/residue: 1.2071 time to fit residues: 478.3880 Evaluate side-chains 280 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 261 time to evaluate : 2.328 ------------------------------------------------------------------------------- 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 69 optimal weight: 3.9990 chunk 141 optimal weight: 0.0970 chunk 273 optimal weight: 4.9990 chunk 198 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 270 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 169 optimal weight: 0.2980 chunk 93 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.141877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.104913 restraints weight = 21546.473| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.33 r_work: 0.3066 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 22984 Z= 0.192 Angle : 0.554 8.404 31218 Z= 0.290 Chirality : 0.040 0.196 3711 Planarity : 0.004 0.049 3879 Dihedral : 9.440 113.433 3631 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.53 % Favored : 98.44 % Rotamer: Outliers : 2.78 % Allowed : 11.53 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.86 (0.15), residues: 2881 helix: 1.73 (0.11), residues: 2144 sheet: -0.70 (0.76), residues: 42 loop : -0.07 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 737 HIS 0.006 0.001 HIS A 801 PHE 0.027 0.002 PHE C 80 TYR 0.021 0.001 TYR A 99 ARG 0.006 0.000 ARG A 205 Details of bonding type rmsd hydrogen bonds : bond 0.05317 ( 1776) hydrogen bonds : angle 4.58154 ( 5208) SS BOND : bond 0.00282 ( 8) SS BOND : angle 2.94063 ( 16) covalent geometry : bond 0.00442 (22976) covalent geometry : angle 0.55057 (31202) *********************** 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 345 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 280 time to evaluate : 3.634 Fit side-chains REVERT: D 23 CYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8507 (m) REVERT: D 94 ASN cc_start: 0.8599 (t0) cc_final: 0.8385 (t160) REVERT: C 108 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8619 (tt0) REVERT: C 134 TYR cc_start: 0.9084 (m-80) cc_final: 0.8852 (m-80) REVERT: E 99 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8630 (mm) REVERT: O 36 GLU cc_start: 0.7790 (tt0) cc_final: 0.7532 (tt0) REVERT: G 50 LEU cc_start: 0.8203 (tp) cc_final: 0.7954 (tt) REVERT: H 59 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8513 (mtp) REVERT: K 124 ARG cc_start: 0.8708 (mtp180) cc_final: 0.8371 (mtp180) REVERT: L 82 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.7918 (pt0) REVERT: B 109 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8077 (tp) REVERT: B 145 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7212 (tp) REVERT: B 175 MET cc_start: 0.6509 (mmm) cc_final: 0.5860 (mpp) REVERT: B 194 ASN cc_start: 0.7755 (m-40) cc_final: 0.7182 (m-40) REVERT: B 258 GLN cc_start: 0.7583 (mp10) cc_final: 0.7353 (mp10) REVERT: B 313 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8337 (tpt) REVERT: A 23 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7110 (tt0) REVERT: A 195 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7006 (mtpp) REVERT: A 746 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8482 (mp) REVERT: A 762 ARG cc_start: 0.7490 (mmt-90) cc_final: 0.6520 (mmp80) outliers start: 65 outliers final: 19 residues processed: 317 average time/residue: 1.5631 time to fit residues: 574.0043 Evaluate side-chains 287 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 257 time to evaluate : 2.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 108 GLU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 59 MET Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain L residue 82 GLN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 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 195 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 46 optimal weight: 0.1980 chunk 17 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN A 210 ASN A 442 ASN A 499 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.147463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.110343 restraints weight = 21712.823| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.37 r_work: 0.3042 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22984 Z= 0.183 Angle : 0.529 8.153 31218 Z= 0.276 Chirality : 0.039 0.172 3711 Planarity : 0.004 0.045 3879 Dihedral : 9.026 112.774 3625 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.42 % Favored : 98.54 % Rotamer: Outliers : 2.48 % Allowed : 13.07 % Favored : 84.46 % 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: 1.74 (0.11), residues: 2149 sheet: -0.73 (0.77), residues: 42 loop : -0.08 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 737 HIS 0.005 0.001 HIS A 801 PHE 0.026 0.002 PHE C 80 TYR 0.023 0.001 TYR A 99 ARG 0.006 0.000 ARG K 153 Details of bonding type rmsd hydrogen bonds : bond 0.05182 ( 1776) hydrogen bonds : angle 4.54877 ( 5208) SS BOND : bond 0.00418 ( 8) SS BOND : angle 2.22237 ( 16) covalent geometry : bond 0.00419 (22976) covalent geometry : angle 0.52633 (31202) *********************** 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 340 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 282 time to evaluate : 4.636 Fit side-chains REVERT: D 23 CYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8498 (m) REVERT: D 94 ASN cc_start: 0.8602 (t0) cc_final: 0.8388 (t160) REVERT: C 86 MET cc_start: 0.8838 (mtp) cc_final: 0.8386 (ttm) REVERT: C 108 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8666 (tt0) REVERT: C 134 TYR cc_start: 0.9078 (m-80) cc_final: 0.8835 (m-80) REVERT: O 36 GLU cc_start: 0.7785 (tt0) cc_final: 0.7466 (tt0) REVERT: G 82 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8445 (pp30) REVERT: H 157 ASP cc_start: 0.7351 (OUTLIER) cc_final: 0.7049 (t70) REVERT: K 124 ARG cc_start: 0.8768 (mtp180) cc_final: 0.8555 (mtp180) REVERT: B 109 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8006 (tp) REVERT: B 145 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7228 (tp) REVERT: B 175 MET cc_start: 0.6533 (mmm) cc_final: 0.5845 (mpp) REVERT: B 181 ARG cc_start: 0.7637 (tmm-80) cc_final: 0.7142 (ttm-80) REVERT: B 194 ASN cc_start: 0.7717 (m-40) cc_final: 0.7121 (m-40) REVERT: B 254 PHE cc_start: 0.7781 (t80) cc_final: 0.7548 (t80) REVERT: B 258 GLN cc_start: 0.7664 (mp10) cc_final: 0.6985 (mt0) REVERT: B 313 MET cc_start: 0.8621 (mmm) cc_final: 0.8322 (tpt) REVERT: A 195 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.6977 (mtpp) REVERT: A 746 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8449 (mp) REVERT: A 762 ARG cc_start: 0.7490 (mmt-90) cc_final: 0.6521 (mmp80) outliers start: 58 outliers final: 23 residues processed: 313 average time/residue: 1.6085 time to fit residues: 589.6367 Evaluate side-chains 296 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 265 time to evaluate : 2.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain 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 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 134 ILE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 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 69 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 167 optimal weight: 2.9990 chunk 267 optimal weight: 0.4980 chunk 170 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 260 optimal weight: 0.9980 chunk 265 optimal weight: 0.9980 chunk 198 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN A 210 ASN A 442 ASN A 499 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.148980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.112022 restraints weight = 21639.474| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.37 r_work: 0.3104 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22984 Z= 0.148 Angle : 0.494 7.863 31218 Z= 0.260 Chirality : 0.038 0.180 3711 Planarity : 0.004 0.044 3879 Dihedral : 8.639 110.455 3625 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.39 % Favored : 98.58 % Rotamer: Outliers : 2.65 % Allowed : 13.83 % Favored : 83.52 % 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: 1.98 (0.15), residues: 2881 helix: 1.75 (0.11), residues: 2184 sheet: -0.80 (0.79), residues: 38 loop : 0.09 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 737 HIS 0.004 0.001 HIS A 801 PHE 0.025 0.001 PHE C 80 TYR 0.024 0.001 TYR A 99 ARG 0.006 0.000 ARG A 205 Details of bonding type rmsd hydrogen bonds : bond 0.04924 ( 1776) hydrogen bonds : angle 4.43944 ( 5208) SS BOND : bond 0.00342 ( 8) SS BOND : angle 1.69443 ( 16) covalent geometry : bond 0.00325 (22976) covalent geometry : angle 0.49290 (31202) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 285 time to evaluate : 2.537 Fit side-chains REVERT: D 23 CYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8451 (m) REVERT: D 94 ASN cc_start: 0.8584 (t0) cc_final: 0.8370 (t160) REVERT: C 108 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8657 (tt0) REVERT: C 134 TYR cc_start: 0.9059 (m-80) cc_final: 0.8800 (m-80) REVERT: M 47 MET cc_start: 0.8528 (ttt) cc_final: 0.8302 (tpt) REVERT: O 36 GLU cc_start: 0.7828 (tt0) cc_final: 0.7548 (tt0) REVERT: H 59 MET cc_start: 0.8668 (mtp) cc_final: 0.8255 (mmt) REVERT: K 153 ARG cc_start: 0.8187 (mtp85) cc_final: 0.7851 (ptm160) REVERT: B 109 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8057 (tp) REVERT: B 145 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7239 (tp) REVERT: B 181 ARG cc_start: 0.7660 (tmm-80) cc_final: 0.7121 (ttm-80) REVERT: B 194 ASN cc_start: 0.7738 (m-40) cc_final: 0.7143 (m-40) REVERT: B 254 PHE cc_start: 0.7833 (t80) cc_final: 0.7483 (t80) REVERT: B 258 GLN cc_start: 0.7572 (mp10) cc_final: 0.6913 (mp10) REVERT: B 313 MET cc_start: 0.8649 (mmm) cc_final: 0.8355 (tpt) REVERT: A 195 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7007 (mtpp) REVERT: A 746 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8447 (mp) REVERT: A 762 ARG cc_start: 0.7433 (mmt-90) cc_final: 0.6479 (mmp80) outliers start: 62 outliers final: 24 residues processed: 322 average time/residue: 1.1969 time to fit residues: 451.3772 Evaluate side-chains 299 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 269 time to evaluate : 2.392 ------------------------------------------------------------------------------- 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 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 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 492 SER Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 746 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 235 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 252 optimal weight: 0.7980 chunk 264 optimal weight: 0.8980 chunk 280 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 97 optimal weight: 0.0020 chunk 244 optimal weight: 0.6980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN O 72 GLN ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN B 244 ASN A 210 ASN A 442 ASN A 499 HIS A 533 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.147981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.111960 restraints weight = 21632.412| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.31 r_work: 0.3129 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22984 Z= 0.141 Angle : 0.494 11.775 31218 Z= 0.259 Chirality : 0.038 0.149 3711 Planarity : 0.004 0.043 3879 Dihedral : 8.378 110.621 3625 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.32 % Favored : 98.65 % Rotamer: Outliers : 2.35 % Allowed : 14.82 % Favored : 82.84 % 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: 2.07 (0.15), residues: 2881 helix: 1.82 (0.11), residues: 2187 sheet: -0.83 (0.80), residues: 38 loop : 0.13 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 737 HIS 0.003 0.000 HIS A 801 PHE 0.024 0.001 PHE C 80 TYR 0.025 0.001 TYR A 99 ARG 0.006 0.000 ARG A 205 Details of bonding type rmsd hydrogen bonds : bond 0.04818 ( 1776) hydrogen bonds : angle 4.39306 ( 5208) SS BOND : bond 0.00579 ( 8) SS BOND : angle 2.27191 ( 16) covalent geometry : bond 0.00305 (22976) covalent geometry : angle 0.49153 (31202) *********************** 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 340 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 285 time to evaluate : 2.264 Fit side-chains REVERT: D 23 CYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8434 (m) REVERT: D 94 ASN cc_start: 0.8570 (t0) cc_final: 0.8348 (t160) REVERT: C 86 MET cc_start: 0.8857 (mtp) cc_final: 0.8491 (ttm) REVERT: C 108 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8572 (tt0) REVERT: C 134 TYR cc_start: 0.9026 (m-80) cc_final: 0.8714 (m-80) REVERT: K 153 ARG cc_start: 0.8320 (mtp85) cc_final: 0.8032 (ptm160) REVERT: B 109 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8023 (tp) REVERT: B 145 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7288 (tp) REVERT: B 181 ARG cc_start: 0.7679 (tmm-80) cc_final: 0.7130 (ttm-80) REVERT: B 194 ASN cc_start: 0.7712 (m-40) cc_final: 0.7142 (m-40) REVERT: B 254 PHE cc_start: 0.7900 (t80) cc_final: 0.7455 (t80) REVERT: B 258 GLN cc_start: 0.7576 (mp10) cc_final: 0.6809 (mp10) REVERT: B 313 MET cc_start: 0.8629 (mmm) cc_final: 0.8341 (tpt) REVERT: A 85 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6842 (mp0) REVERT: A 195 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7046 (mtpp) REVERT: A 746 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8452 (mp) REVERT: A 753 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7624 (mmm) REVERT: A 762 ARG cc_start: 0.7437 (mmt-90) cc_final: 0.6402 (mmp80) outliers start: 55 outliers final: 26 residues processed: 316 average time/residue: 1.1543 time to fit residues: 426.6918 Evaluate side-chains 305 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 271 time to evaluate : 2.571 ------------------------------------------------------------------------------- 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 E residue 131 LEU 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 45 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 B residue 34 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 753 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 144 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 251 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 267 optimal weight: 0.0570 chunk 105 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 ASN C 46 ASN ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN A 442 ASN A 499 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.150260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.114448 restraints weight = 21509.270| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.33 r_work: 0.3177 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22984 Z= 0.157 Angle : 0.507 9.724 31218 Z= 0.265 Chirality : 0.039 0.161 3711 Planarity : 0.004 0.043 3879 Dihedral : 8.279 112.078 3625 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.49 % Favored : 98.47 % Rotamer: Outliers : 2.56 % Allowed : 14.90 % Favored : 82.54 % 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: 2.03 (0.15), residues: 2881 helix: 1.79 (0.11), residues: 2187 sheet: -0.87 (0.80), residues: 38 loop : 0.12 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 204 HIS 0.004 0.001 HIS A 801 PHE 0.027 0.001 PHE A 774 TYR 0.029 0.001 TYR L 66 ARG 0.005 0.000 ARG A 205 Details of bonding type rmsd hydrogen bonds : bond 0.04901 ( 1776) hydrogen bonds : angle 4.42356 ( 5208) SS BOND : bond 0.00241 ( 8) SS BOND : angle 2.43212 ( 16) covalent geometry : bond 0.00352 (22976) covalent geometry : angle 0.50434 (31202) *********************** 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 347 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 287 time to evaluate : 2.425 Fit side-chains REVERT: D 23 CYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8449 (m) REVERT: C 86 MET cc_start: 0.8841 (mtp) cc_final: 0.8447 (ttm) REVERT: C 108 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8588 (tt0) REVERT: C 134 TYR cc_start: 0.9066 (m-80) cc_final: 0.8830 (m-80) REVERT: G 125 LEU cc_start: 0.8217 (tp) cc_final: 0.7995 (tt) REVERT: H 157 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6912 (t70) REVERT: K 153 ARG cc_start: 0.8440 (mtp85) cc_final: 0.7954 (ptm160) REVERT: B 109 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8014 (tp) REVERT: B 145 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7250 (tp) REVERT: B 150 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7161 (mm-30) REVERT: B 181 ARG cc_start: 0.7706 (tmm-80) cc_final: 0.7128 (ttm-80) REVERT: B 194 ASN cc_start: 0.7684 (m-40) cc_final: 0.7093 (m-40) REVERT: B 254 PHE cc_start: 0.7859 (t80) cc_final: 0.7418 (t80) REVERT: B 258 GLN cc_start: 0.7538 (mp10) cc_final: 0.6831 (mp10) REVERT: A 85 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6845 (mp0) REVERT: A 195 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7044 (mtpp) REVERT: A 746 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8450 (mp) REVERT: A 753 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7580 (mmm) REVERT: A 762 ARG cc_start: 0.7442 (mmt-90) cc_final: 0.6347 (mmp80) outliers start: 60 outliers final: 27 residues processed: 320 average time/residue: 1.1549 time to fit residues: 433.5727 Evaluate side-chains 310 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 274 time to evaluate : 2.347 ------------------------------------------------------------------------------- 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 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 54 THR Chi-restraints excluded: chain A residue 85 GLU 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 492 SER Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 753 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 240 optimal weight: 2.9990 chunk 224 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 chunk 257 optimal weight: 0.7980 chunk 232 optimal weight: 7.9990 chunk 241 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 250 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 53 ASN ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN A 499 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.151485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.116274 restraints weight = 21901.676| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.31 r_work: 0.3083 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22984 Z= 0.157 Angle : 0.509 9.200 31218 Z= 0.265 Chirality : 0.038 0.158 3711 Planarity : 0.004 0.043 3879 Dihedral : 8.211 112.762 3625 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.42 % Favored : 98.54 % Rotamer: Outliers : 2.35 % Allowed : 15.54 % Favored : 82.11 % 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: 2.03 (0.15), residues: 2881 helix: 1.79 (0.11), residues: 2187 sheet: -0.93 (0.80), residues: 38 loop : 0.11 (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 0.032 0.001 TYR L 66 ARG 0.005 0.000 ARG A 205 Details of bonding type rmsd hydrogen bonds : bond 0.04898 ( 1776) hydrogen bonds : angle 4.42939 ( 5208) SS BOND : bond 0.00191 ( 8) SS BOND : angle 2.38910 ( 16) covalent geometry : bond 0.00353 (22976) covalent geometry : angle 0.50591 (31202) *********************** 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 338 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 283 time to evaluate : 2.325 Fit side-chains REVERT: D 23 CYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8473 (m) REVERT: C 86 MET cc_start: 0.8864 (mtp) cc_final: 0.8476 (ttm) REVERT: C 108 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8583 (tt0) REVERT: C 134 TYR cc_start: 0.9078 (m-80) cc_final: 0.8837 (m-80) REVERT: G 125 LEU cc_start: 0.8263 (tp) cc_final: 0.8042 (tt) REVERT: H 157 ASP cc_start: 0.7192 (OUTLIER) cc_final: 0.6936 (t70) REVERT: J 156 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.6728 (tt0) REVERT: K 153 ARG cc_start: 0.8305 (mtp85) cc_final: 0.7915 (ptm160) REVERT: B 109 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8095 (tp) REVERT: B 145 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7293 (tp) REVERT: B 181 ARG cc_start: 0.7757 (tmm-80) cc_final: 0.7179 (ttm-80) REVERT: B 194 ASN cc_start: 0.7758 (m-40) cc_final: 0.7179 (m-40) REVERT: B 254 PHE cc_start: 0.7943 (t80) cc_final: 0.7473 (t80) REVERT: B 258 GLN cc_start: 0.7593 (mp10) cc_final: 0.6859 (mp10) REVERT: A 85 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6850 (mp0) REVERT: A 195 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7096 (mtpp) REVERT: A 746 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8555 (mp) REVERT: A 753 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7619 (mmm) REVERT: A 762 ARG cc_start: 0.7497 (mmt-90) cc_final: 0.6433 (mmp80) outliers start: 55 outliers final: 32 residues processed: 314 average time/residue: 1.1245 time to fit residues: 415.3091 Evaluate side-chains 322 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 280 time to evaluate : 2.382 ------------------------------------------------------------------------------- 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 K residue 138 VAL Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 145 ILE Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 776 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 271 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 202 optimal weight: 0.5980 chunk 235 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 151 optimal weight: 0.7980 chunk 279 optimal weight: 3.9990 chunk 236 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 15 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 ASN ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN A 499 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.153735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.118996 restraints weight = 21773.323| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.30 r_work: 0.3150 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22984 Z= 0.150 Angle : 0.504 8.751 31218 Z= 0.263 Chirality : 0.038 0.153 3711 Planarity : 0.004 0.042 3879 Dihedral : 8.160 112.771 3625 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.35 % Favored : 98.61 % Rotamer: Outliers : 1.92 % Allowed : 16.23 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.08 (0.15), residues: 2881 helix: 1.82 (0.11), residues: 2187 sheet: -0.94 (0.79), residues: 38 loop : 0.15 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 204 HIS 0.004 0.001 HIS A 801 PHE 0.025 0.001 PHE C 80 TYR 0.036 0.001 TYR L 66 ARG 0.007 0.000 ARG A 352 Details of bonding type rmsd hydrogen bonds : bond 0.04845 ( 1776) hydrogen bonds : angle 4.41112 ( 5208) SS BOND : bond 0.00187 ( 8) SS BOND : angle 2.26791 ( 16) covalent geometry : bond 0.00335 (22976) covalent geometry : angle 0.50141 (31202) *********************** 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 333 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 288 time to evaluate : 2.363 Fit side-chains REVERT: D 23 CYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8504 (m) REVERT: C 86 MET cc_start: 0.8865 (mtp) cc_final: 0.8482 (ttm) REVERT: C 108 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8590 (tt0) REVERT: C 134 TYR cc_start: 0.9070 (m-80) cc_final: 0.8825 (m-80) REVERT: G 125 LEU cc_start: 0.8224 (tp) cc_final: 0.8003 (tt) REVERT: H 59 MET cc_start: 0.8854 (mmm) cc_final: 0.8228 (mmt) REVERT: H 157 ASP cc_start: 0.7193 (OUTLIER) cc_final: 0.6936 (t70) REVERT: J 3 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7594 (tt0) REVERT: K 153 ARG cc_start: 0.8408 (mtp85) cc_final: 0.7946 (ptm160) REVERT: B 109 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8013 (tp) REVERT: B 145 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7270 (tp) REVERT: B 181 ARG cc_start: 0.7767 (tmm-80) cc_final: 0.7190 (ttm-80) REVERT: B 194 ASN cc_start: 0.7794 (m-40) cc_final: 0.7209 (m-40) REVERT: B 254 PHE cc_start: 0.7934 (t80) cc_final: 0.7448 (t80) REVERT: B 258 GLN cc_start: 0.7630 (mp10) cc_final: 0.6893 (mp10) REVERT: B 334 GLN cc_start: 0.7503 (mp10) cc_final: 0.6230 (pp30) REVERT: A 85 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: A 195 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7079 (mtpp) REVERT: A 746 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8546 (mp) REVERT: A 753 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7635 (mmm) REVERT: A 762 ARG cc_start: 0.7480 (mmt-90) cc_final: 0.6383 (mmp80) outliers start: 45 outliers final: 32 residues processed: 316 average time/residue: 1.1880 time to fit residues: 436.3109 Evaluate side-chains 319 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 278 time to evaluate : 2.315 ------------------------------------------------------------------------------- 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 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 54 THR Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 776 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 198 optimal weight: 6.9990 chunk 220 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 210 optimal weight: 0.6980 chunk 214 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 chunk 255 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 250 optimal weight: 0.9980 chunk 272 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN A 499 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.150646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.115429 restraints weight = 22008.704| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.31 r_work: 0.3274 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22984 Z= 0.151 Angle : 0.505 8.651 31218 Z= 0.264 Chirality : 0.038 0.151 3711 Planarity : 0.004 0.042 3879 Dihedral : 8.129 113.180 3625 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.35 % Favored : 98.61 % Rotamer: Outliers : 1.92 % Allowed : 16.27 % 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: 2.09 (0.15), residues: 2881 helix: 1.83 (0.11), residues: 2187 sheet: -0.96 (0.79), residues: 38 loop : 0.16 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 204 HIS 0.004 0.001 HIS A 801 PHE 0.025 0.001 PHE C 80 TYR 0.037 0.001 TYR L 66 ARG 0.007 0.000 ARG A 352 Details of bonding type rmsd hydrogen bonds : bond 0.04837 ( 1776) hydrogen bonds : angle 4.41398 ( 5208) SS BOND : bond 0.00197 ( 8) SS BOND : angle 2.24110 ( 16) covalent geometry : bond 0.00335 (22976) covalent geometry : angle 0.50246 (31202) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 280 time to evaluate : 2.457 Fit side-chains REVERT: D 23 CYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8515 (m) REVERT: C 86 MET cc_start: 0.8869 (mtp) cc_final: 0.8467 (ttm) REVERT: C 108 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8595 (tt0) REVERT: C 134 TYR cc_start: 0.9073 (m-80) cc_final: 0.8783 (m-80) REVERT: G 125 LEU cc_start: 0.8277 (tp) cc_final: 0.8066 (tt) REVERT: H 157 ASP cc_start: 0.7210 (OUTLIER) cc_final: 0.6961 (t70) REVERT: J 3 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7576 (tt0) REVERT: K 131 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8384 (mm) REVERT: K 153 ARG cc_start: 0.8360 (mtp85) cc_final: 0.8088 (ptm160) REVERT: L 46 ARG cc_start: 0.8603 (mmm-85) cc_final: 0.8198 (mtp180) REVERT: B 109 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8122 (tp) REVERT: B 145 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7338 (tp) REVERT: B 175 MET cc_start: 0.6413 (mmp) cc_final: 0.6151 (mmm) REVERT: B 181 ARG cc_start: 0.7816 (tmm-80) cc_final: 0.7156 (ttm-80) REVERT: B 194 ASN cc_start: 0.7821 (m-40) cc_final: 0.7263 (m-40) REVERT: B 254 PHE cc_start: 0.7989 (t80) cc_final: 0.7506 (t80) REVERT: B 258 GLN cc_start: 0.7730 (mp10) cc_final: 0.6967 (mp10) REVERT: A 85 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.6902 (mp0) REVERT: A 195 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7121 (mtpp) REVERT: A 247 LYS cc_start: 0.8244 (tppt) cc_final: 0.8044 (tppp) REVERT: A 442 ASN cc_start: 0.7750 (m110) cc_final: 0.7236 (p0) REVERT: A 746 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8580 (mp) REVERT: A 753 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7649 (mmm) REVERT: A 762 ARG cc_start: 0.7525 (mmt-90) cc_final: 0.6459 (mmp80) outliers start: 45 outliers final: 27 residues processed: 306 average time/residue: 1.3002 time to fit residues: 472.0804 Evaluate side-chains 317 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 280 time to evaluate : 2.500 ------------------------------------------------------------------------------- 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 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 145 ILE Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 753 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 129 optimal weight: 2.9990 chunk 274 optimal weight: 1.9990 chunk 87 optimal weight: 0.0970 chunk 154 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 263 optimal weight: 0.0980 chunk 156 optimal weight: 0.9990 chunk 258 optimal weight: 0.9980 chunk 266 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 GLN ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN A 499 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.154624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.120027 restraints weight = 21749.750| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.30 r_work: 0.3190 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22984 Z= 0.141 Angle : 0.497 8.264 31218 Z= 0.260 Chirality : 0.038 0.149 3711 Planarity : 0.004 0.042 3879 Dihedral : 8.052 112.747 3625 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.28 % Favored : 98.68 % Rotamer: Outliers : 2.01 % Allowed : 16.10 % Favored : 81.90 % 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: 2.15 (0.15), residues: 2881 helix: 1.88 (0.11), residues: 2187 sheet: -0.95 (0.78), residues: 38 loop : 0.17 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 204 HIS 0.003 0.000 HIS A 801 PHE 0.024 0.001 PHE C 80 TYR 0.035 0.001 TYR L 66 ARG 0.007 0.000 ARG A 352 Details of bonding type rmsd hydrogen bonds : bond 0.04741 ( 1776) hydrogen bonds : angle 4.37238 ( 5208) SS BOND : bond 0.00177 ( 8) SS BOND : angle 2.10312 ( 16) covalent geometry : bond 0.00308 (22976) covalent geometry : angle 0.49454 (31202) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15339.80 seconds wall clock time: 266 minutes 45.47 seconds (16005.47 seconds total)