Starting phenix.real_space_refine on Mon Mar 18 07:26:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl2_16710/03_2024/8cl2_16710.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl2_16710/03_2024/8cl2_16710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl2_16710/03_2024/8cl2_16710.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl2_16710/03_2024/8cl2_16710.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl2_16710/03_2024/8cl2_16710.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl2_16710/03_2024/8cl2_16710.pdb" } resolution = 3.45 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= 0.002 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6995 atoms to isotropic. 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 115 5.16 5 C 8400 2.51 5 N 2285 2.21 5 O 2535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13335 Number of models: 1 Model: "" Number of chains: 15 Chain: "B" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 527 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 4, 'TRANS': 62} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 514 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "A" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1626 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 527 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 4, 'TRANS': 62} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 514 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "F" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1626 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "G" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 527 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 4, 'TRANS': 62} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 514 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "I" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1626 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "J" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 527 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 4, 'TRANS': 62} Chain: "K" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 514 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "L" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1626 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "M" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 527 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 4, 'TRANS': 62} Chain: "N" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 514 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "O" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1626 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 38 Time building chain proxies: 6.79, per 1000 atoms: 0.51 Number of scatterers: 13335 At special positions: 0 Unit cell: (159.96, 155.31, 93.93, 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 115 16.00 O 2535 8.00 N 2285 7.00 C 8400 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.56 Conformation dependent library (CDL) restraints added in 2.3 seconds 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3250 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 5 sheets defined 75.4% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'B' and resid 160 through 175 removed outlier: 3.855A pdb=" N ALA B 174 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 193 removed outlier: 4.035A pdb=" N LEU B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 removed outlier: 3.559A pdb=" N ALA B 204 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 219 Processing helix chain 'C' and resid 160 through 175 removed outlier: 3.748A pdb=" N ALA C 174 " --> pdb=" O LYS C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 193 removed outlier: 4.245A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 204 removed outlier: 3.807A pdb=" N ALA C 204 " --> pdb=" O THR C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 219 Processing helix chain 'A' and resid 16 through 30 removed outlier: 3.576A pdb=" N LYS A 30 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 57 Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 125 through 145 removed outlier: 4.027A pdb=" N ARG A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 160 through 175 removed outlier: 3.564A pdb=" N ALA A 174 " --> pdb=" O LYS A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 removed outlier: 3.702A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 removed outlier: 3.724A pdb=" N LEU A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'D' and resid 160 through 175 removed outlier: 3.855A pdb=" N ALA D 174 " --> pdb=" O LYS D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 193 removed outlier: 4.036A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.559A pdb=" N ALA D 204 " --> pdb=" O THR D 200 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU D 205 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY D 206 " --> pdb=" O LEU D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 219 Processing helix chain 'E' and resid 160 through 175 removed outlier: 3.749A pdb=" N ALA E 174 " --> pdb=" O LYS E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 193 removed outlier: 4.245A pdb=" N VAL E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 204 removed outlier: 3.807A pdb=" N ALA E 204 " --> pdb=" O THR E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 219 Processing helix chain 'F' and resid 16 through 30 removed outlier: 3.577A pdb=" N LYS F 30 " --> pdb=" O VAL F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 44 Processing helix chain 'F' and resid 48 through 57 Processing helix chain 'F' and resid 62 through 84 Processing helix chain 'F' and resid 100 through 105 Processing helix chain 'F' and resid 110 through 120 Processing helix chain 'F' and resid 125 through 145 removed outlier: 4.028A pdb=" N ARG F 132 " --> pdb=" O GLU F 128 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP F 133 " --> pdb=" O ILE F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 153 Processing helix chain 'F' and resid 160 through 175 removed outlier: 3.565A pdb=" N ALA F 174 " --> pdb=" O LYS F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 193 removed outlier: 3.702A pdb=" N VAL F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 205 removed outlier: 3.724A pdb=" N LEU F 205 " --> pdb=" O ILE F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 219 Processing helix chain 'G' and resid 160 through 175 removed outlier: 3.855A pdb=" N ALA G 174 " --> pdb=" O LYS G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 193 removed outlier: 4.036A pdb=" N LEU G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL G 191 " --> pdb=" O GLU G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 removed outlier: 3.559A pdb=" N ALA G 204 " --> pdb=" O THR G 200 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU G 205 " --> pdb=" O ILE G 201 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY G 206 " --> pdb=" O LEU G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 219 Processing helix chain 'H' and resid 160 through 175 removed outlier: 3.748A pdb=" N ALA H 174 " --> pdb=" O LYS H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 193 removed outlier: 4.245A pdb=" N VAL H 191 " --> pdb=" O GLU H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 204 removed outlier: 3.807A pdb=" N ALA H 204 " --> pdb=" O THR H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 219 Processing helix chain 'I' and resid 16 through 30 removed outlier: 3.576A pdb=" N LYS I 30 " --> pdb=" O VAL I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 44 Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 62 through 84 Processing helix chain 'I' and resid 100 through 105 Processing helix chain 'I' and resid 110 through 120 Processing helix chain 'I' and resid 125 through 145 removed outlier: 4.028A pdb=" N ARG I 132 " --> pdb=" O GLU I 128 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP I 133 " --> pdb=" O ILE I 129 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 153 Processing helix chain 'I' and resid 160 through 175 removed outlier: 3.564A pdb=" N ALA I 174 " --> pdb=" O LYS I 170 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 193 removed outlier: 3.703A pdb=" N VAL I 191 " --> pdb=" O GLU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 205 removed outlier: 3.724A pdb=" N LEU I 205 " --> pdb=" O ILE I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 219 Processing helix chain 'J' and resid 160 through 175 removed outlier: 3.855A pdb=" N ALA J 174 " --> pdb=" O LYS J 170 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 193 removed outlier: 4.035A pdb=" N LEU J 190 " --> pdb=" O THR J 186 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL J 191 " --> pdb=" O GLU J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 206 removed outlier: 3.559A pdb=" N ALA J 204 " --> pdb=" O THR J 200 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU J 205 " --> pdb=" O ILE J 201 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY J 206 " --> pdb=" O LEU J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 219 Processing helix chain 'K' and resid 160 through 175 removed outlier: 3.748A pdb=" N ALA K 174 " --> pdb=" O LYS K 170 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 193 removed outlier: 4.246A pdb=" N VAL K 191 " --> pdb=" O GLU K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 204 removed outlier: 3.807A pdb=" N ALA K 204 " --> pdb=" O THR K 200 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 219 Processing helix chain 'L' and resid 16 through 30 removed outlier: 3.576A pdb=" N LYS L 30 " --> pdb=" O VAL L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 44 Processing helix chain 'L' and resid 48 through 57 Processing helix chain 'L' and resid 62 through 84 Processing helix chain 'L' and resid 100 through 105 Processing helix chain 'L' and resid 110 through 120 Processing helix chain 'L' and resid 125 through 145 removed outlier: 4.027A pdb=" N ARG L 132 " --> pdb=" O GLU L 128 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP L 133 " --> pdb=" O ILE L 129 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 153 Processing helix chain 'L' and resid 160 through 175 removed outlier: 3.565A pdb=" N ALA L 174 " --> pdb=" O LYS L 170 " (cutoff:3.500A) Processing helix chain 'L' and resid 178 through 193 removed outlier: 3.703A pdb=" N VAL L 191 " --> pdb=" O GLU L 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 205 removed outlier: 3.724A pdb=" N LEU L 205 " --> pdb=" O ILE L 201 " (cutoff:3.500A) Processing helix chain 'L' and resid 210 through 219 Processing helix chain 'M' and resid 160 through 175 removed outlier: 3.855A pdb=" N ALA M 174 " --> pdb=" O LYS M 170 " (cutoff:3.500A) Processing helix chain 'M' and resid 178 through 193 removed outlier: 4.036A pdb=" N LEU M 190 " --> pdb=" O THR M 186 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL M 191 " --> pdb=" O GLU M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 206 removed outlier: 3.559A pdb=" N ALA M 204 " --> pdb=" O THR M 200 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU M 205 " --> pdb=" O ILE M 201 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY M 206 " --> pdb=" O LEU M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 219 Processing helix chain 'N' and resid 160 through 175 removed outlier: 3.748A pdb=" N ALA N 174 " --> pdb=" O LYS N 170 " (cutoff:3.500A) Processing helix chain 'N' and resid 178 through 193 removed outlier: 4.245A pdb=" N VAL N 191 " --> pdb=" O GLU N 187 " (cutoff:3.500A) Processing helix chain 'N' and resid 195 through 204 removed outlier: 3.807A pdb=" N ALA N 204 " --> pdb=" O THR N 200 " (cutoff:3.500A) Processing helix chain 'N' and resid 210 through 219 Processing helix chain 'O' and resid 16 through 30 removed outlier: 3.576A pdb=" N LYS O 30 " --> pdb=" O VAL O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 35 through 44 Processing helix chain 'O' and resid 48 through 57 Processing helix chain 'O' and resid 62 through 84 Processing helix chain 'O' and resid 100 through 105 Processing helix chain 'O' and resid 110 through 120 Processing helix chain 'O' and resid 125 through 145 removed outlier: 4.027A pdb=" N ARG O 132 " --> pdb=" O GLU O 128 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP O 133 " --> pdb=" O ILE O 129 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 153 Processing helix chain 'O' and resid 160 through 175 removed outlier: 3.565A pdb=" N ALA O 174 " --> pdb=" O LYS O 170 " (cutoff:3.500A) Processing helix chain 'O' and resid 178 through 193 removed outlier: 3.703A pdb=" N VAL O 191 " --> pdb=" O GLU O 187 " (cutoff:3.500A) Processing helix chain 'O' and resid 195 through 205 removed outlier: 3.724A pdb=" N LEU O 205 " --> pdb=" O ILE O 201 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 219 Processing sheet with id= 1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id= 2, first strand: chain 'F' and resid 2 through 4 Processing sheet with id= 3, first strand: chain 'I' and resid 2 through 4 Processing sheet with id= 4, first strand: chain 'L' and resid 2 through 4 Processing sheet with id= 5, first strand: chain 'O' and resid 2 through 4 840 hydrogen bonds defined for protein. 2490 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.58 Time building geometry restraints manager: 5.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4410 1.34 - 1.46: 1422 1.46 - 1.57: 7563 1.57 - 1.69: 0 1.69 - 1.81: 200 Bond restraints: 13595 Sorted by residual: bond pdb=" CB PRO I 1 " pdb=" CG PRO I 1 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.58e+00 bond pdb=" CB PRO O 1 " pdb=" CG PRO O 1 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.57e+00 bond pdb=" CB PRO F 1 " pdb=" CG PRO F 1 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.57e+00 bond pdb=" CB PRO L 1 " pdb=" CG PRO L 1 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.57e+00 bond pdb=" CB PRO A 1 " pdb=" CG PRO A 1 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.56e+00 ... (remaining 13590 not shown) Histogram of bond angle deviations from ideal: 98.66 - 105.77: 530 105.77 - 112.87: 6988 112.87 - 119.98: 5150 119.98 - 127.09: 5571 127.09 - 134.19: 201 Bond angle restraints: 18440 Sorted by residual: angle pdb=" N ALA O 177 " pdb=" CA ALA O 177 " pdb=" C ALA O 177 " ideal model delta sigma weight residual 110.24 114.10 -3.86 1.47e+00 4.63e-01 6.89e+00 angle pdb=" N ALA A 177 " pdb=" CA ALA A 177 " pdb=" C ALA A 177 " ideal model delta sigma weight residual 110.24 114.08 -3.84 1.47e+00 4.63e-01 6.84e+00 angle pdb=" N ALA I 177 " pdb=" CA ALA I 177 " pdb=" C ALA I 177 " ideal model delta sigma weight residual 110.24 114.08 -3.84 1.47e+00 4.63e-01 6.84e+00 angle pdb=" N ALA F 177 " pdb=" CA ALA F 177 " pdb=" C ALA F 177 " ideal model delta sigma weight residual 110.24 114.08 -3.84 1.47e+00 4.63e-01 6.81e+00 angle pdb=" N ALA L 177 " pdb=" CA ALA L 177 " pdb=" C ALA L 177 " ideal model delta sigma weight residual 110.24 114.07 -3.83 1.47e+00 4.63e-01 6.78e+00 ... (remaining 18435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.68: 7740 15.68 - 31.37: 450 31.37 - 47.05: 120 47.05 - 62.74: 30 62.74 - 78.42: 20 Dihedral angle restraints: 8360 sinusoidal: 3365 harmonic: 4995 Sorted by residual: dihedral pdb=" CA GLU H 175 " pdb=" C GLU H 175 " pdb=" N GLN H 176 " pdb=" CA GLN H 176 " ideal model delta harmonic sigma weight residual -180.00 -150.43 -29.57 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA GLU E 175 " pdb=" C GLU E 175 " pdb=" N GLN E 176 " pdb=" CA GLN E 176 " ideal model delta harmonic sigma weight residual -180.00 -150.44 -29.56 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA GLU C 175 " pdb=" C GLU C 175 " pdb=" N GLN C 176 " pdb=" CA GLN C 176 " ideal model delta harmonic sigma weight residual -180.00 -150.45 -29.55 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 8357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1130 0.033 - 0.065: 610 0.065 - 0.098: 225 0.098 - 0.131: 97 0.131 - 0.164: 23 Chirality restraints: 2085 Sorted by residual: chirality pdb=" CA LYS I 30 " pdb=" N LYS I 30 " pdb=" C LYS I 30 " pdb=" CB LYS I 30 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" CA LYS A 30 " pdb=" N LYS A 30 " pdb=" C LYS A 30 " pdb=" CB LYS A 30 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.60e-01 chirality pdb=" CA LYS L 30 " pdb=" N LYS L 30 " pdb=" C LYS L 30 " pdb=" CB LYS L 30 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.51e-01 ... (remaining 2082 not shown) Planarity restraints: 2390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR L 186 " 0.024 2.00e-02 2.50e+03 4.74e-02 2.25e+01 pdb=" C THR L 186 " -0.082 2.00e-02 2.50e+03 pdb=" O THR L 186 " 0.031 2.00e-02 2.50e+03 pdb=" N GLU L 187 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR I 186 " 0.024 2.00e-02 2.50e+03 4.74e-02 2.24e+01 pdb=" C THR I 186 " -0.082 2.00e-02 2.50e+03 pdb=" O THR I 186 " 0.031 2.00e-02 2.50e+03 pdb=" N GLU I 187 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 186 " -0.024 2.00e-02 2.50e+03 4.74e-02 2.24e+01 pdb=" C THR A 186 " 0.082 2.00e-02 2.50e+03 pdb=" O THR A 186 " -0.031 2.00e-02 2.50e+03 pdb=" N GLU A 187 " -0.028 2.00e-02 2.50e+03 ... (remaining 2387 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 788 2.73 - 3.28: 14664 3.28 - 3.82: 21424 3.82 - 4.36: 26734 4.36 - 4.90: 43362 Nonbonded interactions: 106972 Sorted by model distance: nonbonded pdb=" NH1 ARG I 173 " pdb=" OE1 GLU L 28 " model vdw 2.192 2.520 nonbonded pdb=" NH1 ARG F 173 " pdb=" OE1 GLU I 28 " model vdw 2.193 2.520 nonbonded pdb=" NH1 ARG A 173 " pdb=" OE1 GLU F 28 " model vdw 2.193 2.520 nonbonded pdb=" OE1 GLU A 28 " pdb=" NH1 ARG O 173 " model vdw 2.193 2.520 nonbonded pdb=" NH1 ARG L 173 " pdb=" OE1 GLU O 28 " model vdw 2.193 2.520 ... (remaining 106967 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' } ncs_group { reference = (chain 'B' and resid 157 through 221) selection = chain 'C' selection = (chain 'D' and resid 157 through 221) selection = chain 'E' selection = (chain 'G' and resid 157 through 221) selection = chain 'H' selection = (chain 'J' and resid 157 through 221) selection = chain 'K' selection = (chain 'M' and resid 157 through 221) selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 11.840 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 35.940 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 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 : 0.004 0.080 13595 Z= 0.287 Angle : 0.824 5.144 18440 Z= 0.497 Chirality : 0.048 0.164 2085 Planarity : 0.009 0.086 2390 Dihedral : 12.071 78.424 5110 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.83 (0.18), residues: 1685 helix: -0.79 (0.13), residues: 1145 sheet: -2.23 (0.57), residues: 45 loop : 0.82 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP O 117 HIS 0.007 0.003 HIS A 12 PHE 0.024 0.003 PHE A 40 TYR 0.014 0.004 TYR O 169 ARG 0.011 0.002 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 681 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 LYS cc_start: 0.8710 (tttm) cc_final: 0.8427 (tppt) REVERT: C 166 ASP cc_start: 0.7844 (m-30) cc_final: 0.7479 (m-30) REVERT: C 183 ASN cc_start: 0.8349 (m-40) cc_final: 0.8040 (m-40) REVERT: C 213 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7483 (mt-10) REVERT: A 41 SER cc_start: 0.9001 (t) cc_final: 0.8262 (p) REVERT: A 117 TRP cc_start: 0.8103 (m-10) cc_final: 0.7749 (m-90) REVERT: A 167 ARG cc_start: 0.7978 (mtp180) cc_final: 0.7727 (mtm-85) REVERT: A 183 ASN cc_start: 0.8615 (m-40) cc_final: 0.8405 (m-40) REVERT: A 192 GLN cc_start: 0.8591 (tp40) cc_final: 0.8216 (tm-30) REVERT: D 159 GLU cc_start: 0.8502 (tt0) cc_final: 0.8102 (tt0) REVERT: D 170 LYS cc_start: 0.8690 (tttm) cc_final: 0.8471 (tppt) REVERT: E 166 ASP cc_start: 0.7870 (m-30) cc_final: 0.7594 (m-30) REVERT: E 168 PHE cc_start: 0.8949 (t80) cc_final: 0.8661 (t80) REVERT: E 213 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7498 (mt-10) REVERT: F 39 MET cc_start: 0.8466 (mtt) cc_final: 0.8230 (mtm) REVERT: F 41 SER cc_start: 0.9200 (t) cc_final: 0.8547 (p) REVERT: F 70 LYS cc_start: 0.8720 (mmmm) cc_final: 0.8518 (mptt) REVERT: F 192 GLN cc_start: 0.8575 (tp40) cc_final: 0.8171 (tm-30) REVERT: G 170 LYS cc_start: 0.8634 (tttm) cc_final: 0.8417 (tppt) REVERT: I 41 SER cc_start: 0.9176 (t) cc_final: 0.8552 (p) REVERT: I 68 MET cc_start: 0.8790 (mtp) cc_final: 0.8313 (mtp) REVERT: I 183 ASN cc_start: 0.8494 (m-40) cc_final: 0.8254 (m-40) REVERT: I 192 GLN cc_start: 0.8505 (tp40) cc_final: 0.8209 (tm-30) REVERT: J 159 GLU cc_start: 0.8524 (tt0) cc_final: 0.8207 (tt0) REVERT: J 170 LYS cc_start: 0.8632 (tttm) cc_final: 0.8365 (tppt) REVERT: K 182 LYS cc_start: 0.8494 (mttt) cc_final: 0.8166 (mttp) REVERT: K 183 ASN cc_start: 0.8337 (m-40) cc_final: 0.7921 (m-40) REVERT: K 192 GLN cc_start: 0.8343 (mt0) cc_final: 0.8085 (tt0) REVERT: K 213 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7486 (mt-10) REVERT: L 25 LYS cc_start: 0.8326 (mttt) cc_final: 0.8102 (mtmt) REVERT: L 41 SER cc_start: 0.9112 (t) cc_final: 0.8401 (p) REVERT: L 183 ASN cc_start: 0.8512 (m-40) cc_final: 0.8091 (m-40) REVERT: L 192 GLN cc_start: 0.8518 (tp40) cc_final: 0.8110 (tm-30) REVERT: L 195 ASN cc_start: 0.8522 (p0) cc_final: 0.8064 (p0) REVERT: L 215 MET cc_start: 0.8794 (mtp) cc_final: 0.8589 (mtm) REVERT: M 170 LYS cc_start: 0.8660 (tttm) cc_final: 0.8402 (tppt) REVERT: N 213 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7530 (mt-10) REVERT: O 39 MET cc_start: 0.8457 (mtt) cc_final: 0.8177 (mtp) REVERT: O 41 SER cc_start: 0.9124 (t) cc_final: 0.8407 (p) REVERT: O 117 TRP cc_start: 0.8111 (m-10) cc_final: 0.7518 (m-90) REVERT: O 183 ASN cc_start: 0.8599 (m-40) cc_final: 0.8372 (m-40) REVERT: O 192 GLN cc_start: 0.8636 (tp40) cc_final: 0.8299 (tm-30) REVERT: O 214 MET cc_start: 0.9045 (mtp) cc_final: 0.8842 (mtm) outliers start: 0 outliers final: 0 residues processed: 681 average time/residue: 0.2834 time to fit residues: 264.0847 Evaluate side-chains 495 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 495 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 1.9990 chunk 125 optimal weight: 0.0050 chunk 69 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 129 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 183 ASN A 219 GLN F 50 GLN I 120 HIS L 179 GLN L 183 ASN M 179 GLN M 219 GLN O 50 GLN O 179 GLN O 183 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13595 Z= 0.211 Angle : 0.619 9.942 18440 Z= 0.321 Chirality : 0.041 0.146 2085 Planarity : 0.005 0.032 2390 Dihedral : 5.169 26.373 1820 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 3.17 % Allowed : 11.06 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.30 (0.19), residues: 1685 helix: 0.86 (0.14), residues: 1160 sheet: -1.84 (0.64), residues: 45 loop : 1.60 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 184 HIS 0.003 0.000 HIS I 120 PHE 0.013 0.002 PHE L 40 TYR 0.016 0.002 TYR H 164 ARG 0.005 0.000 ARG L 82 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 552 time to evaluate : 1.576 Fit side-chains revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8275 (tp30) cc_final: 0.7961 (tp30) REVERT: C 166 ASP cc_start: 0.7706 (m-30) cc_final: 0.7293 (m-30) REVERT: C 168 PHE cc_start: 0.8787 (t80) cc_final: 0.8272 (t80) REVERT: C 200 THR cc_start: 0.8694 (m) cc_final: 0.8450 (p) REVERT: A 210 THR cc_start: 0.9347 (p) cc_final: 0.9047 (p) REVERT: D 170 LYS cc_start: 0.8545 (tttm) cc_final: 0.8341 (tppt) REVERT: E 166 ASP cc_start: 0.7983 (m-30) cc_final: 0.7695 (m-30) REVERT: E 171 THR cc_start: 0.8724 (m) cc_final: 0.8503 (p) REVERT: F 70 LYS cc_start: 0.8669 (mmmm) cc_final: 0.8412 (mmtm) REVERT: F 195 ASN cc_start: 0.8633 (p0) cc_final: 0.8416 (p0) REVERT: F 199 LYS cc_start: 0.9053 (tttt) cc_final: 0.8846 (ttmt) REVERT: I 210 THR cc_start: 0.9342 (p) cc_final: 0.9024 (p) REVERT: K 167 ARG cc_start: 0.8238 (mtp85) cc_final: 0.7951 (mtp85) REVERT: L 195 ASN cc_start: 0.8624 (p0) cc_final: 0.8336 (p0) REVERT: L 213 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8027 (mp0) REVERT: M 170 LYS cc_start: 0.8533 (tttm) cc_final: 0.8318 (tppt) REVERT: N 170 LYS cc_start: 0.8693 (ttpp) cc_final: 0.8401 (ttmm) REVERT: N 213 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7503 (mt-10) outliers start: 45 outliers final: 29 residues processed: 580 average time/residue: 0.2856 time to fit residues: 227.7371 Evaluate side-chains 507 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 478 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 197 ASP Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 178 SER Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain M residue 216 THR Chi-restraints excluded: chain N residue 197 ASP Chi-restraints excluded: chain O residue 63 GLN Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain O residue 178 SER Chi-restraints excluded: chain O residue 188 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 150 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 148 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 50 GLN A 179 GLN E 192 GLN I 120 HIS J 155 GLN M 219 GLN O 176 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13595 Z= 0.288 Angle : 0.594 8.798 18440 Z= 0.310 Chirality : 0.042 0.151 2085 Planarity : 0.005 0.036 2390 Dihedral : 4.880 21.475 1820 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.24 % Allowed : 14.79 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.45 (0.19), residues: 1685 helix: 1.01 (0.14), residues: 1165 sheet: -1.94 (0.67), residues: 45 loop : 1.55 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 184 HIS 0.003 0.000 HIS I 120 PHE 0.022 0.002 PHE H 168 TYR 0.008 0.001 TYR O 130 ARG 0.004 0.000 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 502 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8377 (tp30) cc_final: 0.8070 (tp30) REVERT: C 166 ASP cc_start: 0.7651 (m-30) cc_final: 0.7301 (m-30) REVERT: C 170 LYS cc_start: 0.8603 (ttpp) cc_final: 0.8373 (ttmm) REVERT: C 200 THR cc_start: 0.8697 (m) cc_final: 0.8458 (p) REVERT: C 201 ILE cc_start: 0.9106 (mm) cc_final: 0.8865 (mt) REVERT: A 192 GLN cc_start: 0.8519 (tm-30) cc_final: 0.7832 (tm-30) REVERT: A 215 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8217 (mtp) REVERT: E 166 ASP cc_start: 0.7686 (m-30) cc_final: 0.7462 (m-30) REVERT: E 168 PHE cc_start: 0.9000 (t80) cc_final: 0.8711 (t80) REVERT: E 213 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7601 (mp0) REVERT: F 70 LYS cc_start: 0.8725 (mmmm) cc_final: 0.8455 (mmtm) REVERT: F 215 MET cc_start: 0.8765 (mtp) cc_final: 0.8500 (mtp) REVERT: I 41 SER cc_start: 0.9167 (t) cc_final: 0.8937 (m) REVERT: K 203 LYS cc_start: 0.8667 (mmtt) cc_final: 0.8465 (mmtp) REVERT: L 192 GLN cc_start: 0.8370 (tm-30) cc_final: 0.7999 (tm-30) REVERT: L 197 ASP cc_start: 0.7821 (p0) cc_final: 0.7474 (p0) REVERT: N 168 PHE cc_start: 0.8459 (t80) cc_final: 0.8213 (t80) REVERT: N 170 LYS cc_start: 0.8721 (ttpp) cc_final: 0.8455 (ttmm) outliers start: 46 outliers final: 36 residues processed: 518 average time/residue: 0.2690 time to fit residues: 192.2047 Evaluate side-chains 500 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 463 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain H residue 197 ASP Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 216 THR Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 178 SER Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain M residue 216 THR Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain N residue 197 ASP Chi-restraints excluded: chain O residue 63 GLN Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain O residue 176 GLN Chi-restraints excluded: chain O residue 178 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 78 optimal weight: 0.0030 chunk 142 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 GLN A 183 ASN H 192 GLN I 179 GLN I 183 ASN L 195 ASN M 219 GLN O 179 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13595 Z= 0.276 Angle : 0.590 7.981 18440 Z= 0.307 Chirality : 0.042 0.161 2085 Planarity : 0.005 0.037 2390 Dihedral : 4.718 22.057 1820 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.52 % Allowed : 15.99 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.43 (0.19), residues: 1685 helix: 1.05 (0.14), residues: 1170 sheet: -1.92 (0.66), residues: 45 loop : 1.39 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 184 HIS 0.001 0.000 HIS F 12 PHE 0.025 0.002 PHE H 168 TYR 0.010 0.001 TYR E 164 ARG 0.004 0.000 ARG O 132 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 476 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 166 ASP cc_start: 0.7650 (m-30) cc_final: 0.7314 (m-30) REVERT: C 200 THR cc_start: 0.8724 (m) cc_final: 0.8509 (p) REVERT: C 201 ILE cc_start: 0.9117 (mm) cc_final: 0.8909 (mm) REVERT: C 213 GLU cc_start: 0.7917 (mp0) cc_final: 0.7536 (mp0) REVERT: A 192 GLN cc_start: 0.8599 (tm-30) cc_final: 0.7932 (tm-30) REVERT: A 215 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8310 (mtp) REVERT: D 199 LYS cc_start: 0.9164 (ttmt) cc_final: 0.8903 (ttmt) REVERT: E 166 ASP cc_start: 0.7660 (m-30) cc_final: 0.7435 (m-30) REVERT: F 70 LYS cc_start: 0.8742 (mmmm) cc_final: 0.8467 (mmtm) REVERT: H 213 GLU cc_start: 0.8095 (mp0) cc_final: 0.7751 (mp0) REVERT: I 41 SER cc_start: 0.9162 (t) cc_final: 0.8923 (m) REVERT: K 203 LYS cc_start: 0.8692 (mmtt) cc_final: 0.8479 (mmtp) REVERT: K 213 GLU cc_start: 0.7996 (mp0) cc_final: 0.7767 (mp0) REVERT: K 215 MET cc_start: 0.8459 (mtp) cc_final: 0.8202 (mtp) REVERT: L 192 GLN cc_start: 0.8373 (tm-30) cc_final: 0.7939 (tm-30) REVERT: L 197 ASP cc_start: 0.7651 (p0) cc_final: 0.7420 (p0) REVERT: N 170 LYS cc_start: 0.8718 (ttpp) cc_final: 0.8434 (ttmm) outliers start: 50 outliers final: 35 residues processed: 492 average time/residue: 0.2717 time to fit residues: 186.8670 Evaluate side-chains 481 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 445 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 197 ASP Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 216 THR Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 197 ASP Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 35 GLU Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain M residue 216 THR Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain N residue 197 ASP Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 63 GLN Chi-restraints excluded: chain O residue 110 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 110 optimal weight: 0.4980 chunk 0 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 GLN C 195 ASN A 195 ASN I 179 GLN O 179 GLN O 183 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13595 Z= 0.204 Angle : 0.545 8.037 18440 Z= 0.283 Chirality : 0.040 0.163 2085 Planarity : 0.005 0.039 2390 Dihedral : 4.490 21.881 1820 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.59 % Allowed : 17.11 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.49 (0.20), residues: 1685 helix: 1.08 (0.15), residues: 1185 sheet: -1.57 (0.68), residues: 45 loop : 1.42 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 184 HIS 0.001 0.000 HIS O 12 PHE 0.017 0.001 PHE E 168 TYR 0.009 0.001 TYR K 164 ARG 0.003 0.000 ARG L 82 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 468 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 166 ASP cc_start: 0.7603 (m-30) cc_final: 0.7262 (m-30) REVERT: C 213 GLU cc_start: 0.7974 (mp0) cc_final: 0.7538 (mp0) REVERT: D 210 THR cc_start: 0.9084 (p) cc_final: 0.8852 (p) REVERT: E 166 ASP cc_start: 0.7636 (m-30) cc_final: 0.7406 (m-30) REVERT: E 213 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7653 (mp0) REVERT: F 70 LYS cc_start: 0.8717 (mmmm) cc_final: 0.8466 (mmtm) REVERT: H 168 PHE cc_start: 0.8725 (t80) cc_final: 0.8177 (t80) REVERT: H 213 GLU cc_start: 0.8095 (mp0) cc_final: 0.7749 (mp0) REVERT: K 203 LYS cc_start: 0.8637 (mmtt) cc_final: 0.8362 (mmtp) REVERT: K 213 GLU cc_start: 0.7994 (mp0) cc_final: 0.7743 (mp0) REVERT: K 215 MET cc_start: 0.8440 (mtp) cc_final: 0.8192 (mtp) REVERT: L 182 LYS cc_start: 0.9024 (mttt) cc_final: 0.8822 (mmmm) REVERT: L 197 ASP cc_start: 0.7646 (p0) cc_final: 0.7236 (p0) REVERT: M 203 LYS cc_start: 0.8473 (mtpp) cc_final: 0.8239 (mtmt) REVERT: N 170 LYS cc_start: 0.8701 (ttpp) cc_final: 0.8433 (ttmm) REVERT: N 213 GLU cc_start: 0.7997 (mp0) cc_final: 0.7622 (mp0) REVERT: O 70 LYS cc_start: 0.8498 (mptt) cc_final: 0.8277 (mptt) REVERT: O 111 LEU cc_start: 0.8370 (tp) cc_final: 0.8142 (mp) REVERT: O 192 GLN cc_start: 0.8335 (tm-30) cc_final: 0.7671 (tm-30) outliers start: 51 outliers final: 30 residues processed: 489 average time/residue: 0.2734 time to fit residues: 190.8945 Evaluate side-chains 475 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 445 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain K residue 197 ASP Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain N residue 159 GLU Chi-restraints excluded: chain N residue 197 ASP Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 63 GLN Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 176 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 93 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 73 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN A 183 ASN E 195 ASN H 195 ASN I 179 GLN I 183 ASN K 195 ASN L 183 ASN N 195 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13595 Z= 0.231 Angle : 0.558 10.491 18440 Z= 0.289 Chirality : 0.041 0.166 2085 Planarity : 0.005 0.039 2390 Dihedral : 4.437 23.322 1820 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.37 % Allowed : 17.96 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.46 (0.20), residues: 1685 helix: 1.11 (0.15), residues: 1180 sheet: -1.29 (0.67), residues: 45 loop : 1.21 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 184 HIS 0.001 0.000 HIS F 12 PHE 0.020 0.002 PHE H 168 TYR 0.009 0.001 TYR E 164 ARG 0.004 0.000 ARG L 82 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 446 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8420 (tp30) cc_final: 0.7978 (tp30) REVERT: C 166 ASP cc_start: 0.7618 (m-30) cc_final: 0.7297 (m-30) REVERT: C 213 GLU cc_start: 0.8106 (mp0) cc_final: 0.7688 (mp0) REVERT: D 210 THR cc_start: 0.9092 (p) cc_final: 0.8870 (p) REVERT: E 166 ASP cc_start: 0.7615 (m-30) cc_final: 0.7399 (m-30) REVERT: E 213 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7678 (mp0) REVERT: F 70 LYS cc_start: 0.8743 (mmmm) cc_final: 0.8469 (mptt) REVERT: H 213 GLU cc_start: 0.8183 (mp0) cc_final: 0.7762 (mp0) REVERT: K 213 GLU cc_start: 0.8105 (mp0) cc_final: 0.7804 (mp0) REVERT: K 215 MET cc_start: 0.8396 (mtp) cc_final: 0.8124 (mtp) REVERT: L 192 GLN cc_start: 0.8400 (tm-30) cc_final: 0.7932 (tm-30) REVERT: L 197 ASP cc_start: 0.7594 (p0) cc_final: 0.7184 (p0) REVERT: M 203 LYS cc_start: 0.8510 (mtpp) cc_final: 0.8227 (mtmt) REVERT: N 170 LYS cc_start: 0.8683 (ttpp) cc_final: 0.8438 (ttmm) REVERT: N 213 GLU cc_start: 0.7936 (mp0) cc_final: 0.7610 (mp0) REVERT: O 111 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8153 (mp) REVERT: O 192 GLN cc_start: 0.8351 (tm-30) cc_final: 0.7628 (tm-30) outliers start: 62 outliers final: 49 residues processed: 470 average time/residue: 0.2599 time to fit residues: 172.0762 Evaluate side-chains 477 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 427 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 214 MET Chi-restraints excluded: chain H residue 197 ASP Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 183 ASN Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 214 MET Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain K residue 197 ASP Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 35 GLU Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain M residue 216 THR Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain N residue 159 GLU Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain N residue 197 ASP Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 111 LEU Chi-restraints excluded: chain O residue 176 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 159 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 195 ASN H 195 ASN I 179 GLN K 195 ASN N 195 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13595 Z= 0.221 Angle : 0.553 9.695 18440 Z= 0.286 Chirality : 0.041 0.166 2085 Planarity : 0.005 0.040 2390 Dihedral : 4.415 23.416 1820 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.23 % Allowed : 18.59 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.44 (0.20), residues: 1685 helix: 1.09 (0.15), residues: 1180 sheet: -1.04 (0.67), residues: 45 loop : 1.19 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 184 HIS 0.001 0.000 HIS F 12 PHE 0.026 0.002 PHE H 168 TYR 0.009 0.001 TYR E 164 ARG 0.009 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 442 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8412 (tp30) cc_final: 0.7978 (tp30) REVERT: C 166 ASP cc_start: 0.7620 (m-30) cc_final: 0.7290 (m-30) REVERT: C 213 GLU cc_start: 0.8122 (mp0) cc_final: 0.7677 (mp0) REVERT: A 192 GLN cc_start: 0.8562 (tm-30) cc_final: 0.8058 (tm-30) REVERT: D 210 THR cc_start: 0.9084 (p) cc_final: 0.8862 (p) REVERT: E 166 ASP cc_start: 0.7617 (m-30) cc_final: 0.7395 (m-30) REVERT: F 70 LYS cc_start: 0.8714 (mmmm) cc_final: 0.8489 (mptt) REVERT: F 111 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8158 (tt) REVERT: H 213 GLU cc_start: 0.8160 (mp0) cc_final: 0.7769 (mp0) REVERT: J 172 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8482 (tp) REVERT: K 213 GLU cc_start: 0.8104 (mp0) cc_final: 0.7819 (mp0) REVERT: L 192 GLN cc_start: 0.8414 (tm-30) cc_final: 0.7949 (tm-30) REVERT: L 197 ASP cc_start: 0.7525 (p0) cc_final: 0.7162 (p0) REVERT: M 203 LYS cc_start: 0.8498 (mtpp) cc_final: 0.8240 (mtmt) REVERT: M 210 THR cc_start: 0.8860 (p) cc_final: 0.8511 (p) REVERT: N 213 GLU cc_start: 0.7872 (mp0) cc_final: 0.7518 (mp0) REVERT: O 39 MET cc_start: 0.8179 (mtt) cc_final: 0.7871 (mtp) REVERT: O 192 GLN cc_start: 0.8350 (tm-30) cc_final: 0.7640 (tm-30) outliers start: 60 outliers final: 51 residues processed: 470 average time/residue: 0.2580 time to fit residues: 171.7194 Evaluate side-chains 474 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 421 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 214 MET Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 214 MET Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain K residue 197 ASP Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 35 GLU Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain M residue 216 THR Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain N residue 159 GLU Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain N residue 197 ASP Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 18 ARG Chi-restraints excluded: chain O residue 63 GLN Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 176 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN E 195 ASN H 195 ASN I 179 GLN I 183 ASN K 195 ASN N 195 ASN O 183 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13595 Z= 0.204 Angle : 0.563 10.535 18440 Z= 0.293 Chirality : 0.041 0.184 2085 Planarity : 0.005 0.039 2390 Dihedral : 4.366 23.413 1820 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 4.30 % Allowed : 19.08 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.52 (0.20), residues: 1685 helix: 1.15 (0.15), residues: 1175 sheet: -0.93 (0.67), residues: 45 loop : 1.19 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 184 HIS 0.001 0.000 HIS F 12 PHE 0.013 0.001 PHE E 168 TYR 0.008 0.001 TYR H 164 ARG 0.008 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 444 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8393 (tp30) cc_final: 0.7938 (tp30) REVERT: C 166 ASP cc_start: 0.7613 (m-30) cc_final: 0.7285 (m-30) REVERT: C 213 GLU cc_start: 0.8125 (mp0) cc_final: 0.7700 (mp0) REVERT: A 192 GLN cc_start: 0.8556 (tm-30) cc_final: 0.8053 (tm-30) REVERT: D 210 THR cc_start: 0.9075 (p) cc_final: 0.7867 (p) REVERT: E 166 ASP cc_start: 0.7606 (m-30) cc_final: 0.7375 (m-30) REVERT: F 70 LYS cc_start: 0.8717 (mmmm) cc_final: 0.8482 (mptt) REVERT: F 111 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8126 (tt) REVERT: H 213 GLU cc_start: 0.8053 (mp0) cc_final: 0.7679 (mp0) REVERT: K 167 ARG cc_start: 0.8286 (mtp85) cc_final: 0.8071 (ttp-110) REVERT: K 213 GLU cc_start: 0.8053 (mp0) cc_final: 0.7819 (mp0) REVERT: L 192 GLN cc_start: 0.8391 (tm-30) cc_final: 0.7968 (tm-30) REVERT: L 197 ASP cc_start: 0.7438 (p0) cc_final: 0.7109 (p0) REVERT: M 203 LYS cc_start: 0.8502 (mtpp) cc_final: 0.8300 (mtmt) REVERT: N 166 ASP cc_start: 0.7515 (m-30) cc_final: 0.7311 (m-30) REVERT: N 168 PHE cc_start: 0.7748 (t80) cc_final: 0.7448 (t80) REVERT: N 213 GLU cc_start: 0.7909 (mp0) cc_final: 0.7590 (mp0) REVERT: O 39 MET cc_start: 0.8164 (mtt) cc_final: 0.7835 (mtp) REVERT: O 192 GLN cc_start: 0.8357 (tm-30) cc_final: 0.7635 (tm-30) outliers start: 61 outliers final: 52 residues processed: 470 average time/residue: 0.2724 time to fit residues: 182.4416 Evaluate side-chains 474 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 421 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 214 MET Chi-restraints excluded: chain H residue 197 ASP Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain K residue 197 ASP Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 35 GLU Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain M residue 216 THR Chi-restraints excluded: chain M residue 218 CYS Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain N residue 159 GLU Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain N residue 197 ASP Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 18 ARG Chi-restraints excluded: chain O residue 63 GLN Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 176 GLN Chi-restraints excluded: chain O residue 210 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 0.0980 chunk 139 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 0.0170 chunk 116 optimal weight: 0.0980 chunk 45 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 chunk 147 optimal weight: 0.4980 chunk 97 optimal weight: 0.4980 overall best weight: 0.2418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 ASN C 195 ASN E 195 ASN G 193 ASN H 195 ASN ** I 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 195 ASN L 179 GLN N 195 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13595 Z= 0.157 Angle : 0.541 11.467 18440 Z= 0.281 Chirality : 0.040 0.165 2085 Planarity : 0.005 0.040 2390 Dihedral : 4.205 21.112 1820 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.54 % Allowed : 21.48 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.64 (0.20), residues: 1685 helix: 1.23 (0.15), residues: 1180 sheet: -0.79 (0.66), residues: 45 loop : 1.26 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 184 HIS 0.005 0.000 HIS I 120 PHE 0.010 0.001 PHE C 168 TYR 0.009 0.001 TYR N 164 ARG 0.004 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 458 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8465 (tp) REVERT: C 213 GLU cc_start: 0.8112 (mp0) cc_final: 0.7668 (mp0) REVERT: A 192 GLN cc_start: 0.8570 (tm-30) cc_final: 0.8027 (tm-30) REVERT: D 210 THR cc_start: 0.8920 (p) cc_final: 0.8697 (p) REVERT: F 45 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7376 (mm-30) REVERT: F 70 LYS cc_start: 0.8734 (mmmm) cc_final: 0.8486 (mptt) REVERT: G 176 GLN cc_start: 0.7786 (mm-40) cc_final: 0.7325 (mm-40) REVERT: H 199 LYS cc_start: 0.8506 (ttpt) cc_final: 0.8193 (ttmt) REVERT: H 213 GLU cc_start: 0.8018 (mp0) cc_final: 0.7701 (mp0) REVERT: I 55 MET cc_start: 0.8523 (mtp) cc_final: 0.8258 (mtp) REVERT: J 172 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8382 (tp) REVERT: J 192 GLN cc_start: 0.8644 (tp40) cc_final: 0.8346 (tp40) REVERT: J 199 LYS cc_start: 0.8931 (ttpt) cc_final: 0.8697 (ttmt) REVERT: K 167 ARG cc_start: 0.8272 (mtp85) cc_final: 0.7950 (mtm-85) REVERT: K 213 GLU cc_start: 0.8076 (mp0) cc_final: 0.7781 (mp0) REVERT: L 192 GLN cc_start: 0.8345 (tm-30) cc_final: 0.7823 (tm-30) REVERT: N 166 ASP cc_start: 0.7456 (m-30) cc_final: 0.6882 (m-30) REVERT: N 213 GLU cc_start: 0.7778 (mp0) cc_final: 0.7540 (mp0) REVERT: O 182 LYS cc_start: 0.8836 (mttt) cc_final: 0.8620 (mmmm) REVERT: O 192 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7536 (tm-30) outliers start: 36 outliers final: 25 residues processed: 478 average time/residue: 0.2481 time to fit residues: 167.9478 Evaluate side-chains 446 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 419 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 214 MET Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain M residue 216 THR Chi-restraints excluded: chain M residue 218 CYS Chi-restraints excluded: chain N residue 221 VAL Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 18 ARG Chi-restraints excluded: chain O residue 210 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 164 optimal weight: 7.9990 chunk 151 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 101 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN A 179 GLN A 183 ASN E 195 ASN ** G 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 ASN I 120 HIS K 195 ASN N 195 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13595 Z= 0.196 Angle : 0.603 11.035 18440 Z= 0.310 Chirality : 0.042 0.163 2085 Planarity : 0.005 0.040 2390 Dihedral : 4.275 22.307 1820 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.04 % Allowed : 21.97 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.54 (0.20), residues: 1685 helix: 1.18 (0.15), residues: 1180 sheet: -0.63 (0.65), residues: 45 loop : 1.14 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 184 HIS 0.006 0.001 HIS I 120 PHE 0.044 0.001 PHE E 168 TYR 0.008 0.001 TYR N 164 ARG 0.004 0.000 ARG I 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 411 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8339 (tp30) cc_final: 0.8005 (tp30) REVERT: C 213 GLU cc_start: 0.8118 (mp0) cc_final: 0.7701 (mp0) REVERT: D 210 THR cc_start: 0.8752 (p) cc_final: 0.8495 (p) REVERT: E 213 GLU cc_start: 0.7615 (mp0) cc_final: 0.7361 (pm20) REVERT: F 45 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7446 (mm-30) REVERT: F 70 LYS cc_start: 0.8786 (mmmm) cc_final: 0.8535 (mptt) REVERT: H 213 GLU cc_start: 0.8039 (mp0) cc_final: 0.7681 (mp0) REVERT: I 55 MET cc_start: 0.8597 (mtp) cc_final: 0.8297 (mtp) REVERT: J 172 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8361 (tp) REVERT: J 192 GLN cc_start: 0.8631 (tp40) cc_final: 0.8372 (tp40) REVERT: J 199 LYS cc_start: 0.8945 (ttpt) cc_final: 0.8730 (ttmt) REVERT: K 167 ARG cc_start: 0.8284 (mtp85) cc_final: 0.7983 (mtm-85) REVERT: K 213 GLU cc_start: 0.8166 (mp0) cc_final: 0.7776 (mp0) REVERT: N 166 ASP cc_start: 0.7501 (m-30) cc_final: 0.6944 (m-30) REVERT: N 213 GLU cc_start: 0.7619 (mp0) cc_final: 0.7407 (mp0) REVERT: O 130 TYR cc_start: 0.9197 (t80) cc_final: 0.8874 (t80) REVERT: O 182 LYS cc_start: 0.8886 (mttt) cc_final: 0.8659 (mmmm) REVERT: O 192 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7609 (tm-30) outliers start: 29 outliers final: 23 residues processed: 432 average time/residue: 0.2619 time to fit residues: 159.0106 Evaluate side-chains 433 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 409 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 214 MET Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 178 SER Chi-restraints excluded: chain M residue 218 CYS Chi-restraints excluded: chain O residue 18 ARG Chi-restraints excluded: chain O residue 176 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.0980 chunk 40 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 24 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN E 195 ASN ** G 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 ASN K 195 ASN L 179 GLN L 183 ASN N 195 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.137642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.103969 restraints weight = 22385.392| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.59 r_work: 0.3203 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.5181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13595 Z= 0.189 Angle : 0.588 12.283 18440 Z= 0.305 Chirality : 0.042 0.174 2085 Planarity : 0.005 0.040 2390 Dihedral : 4.253 22.743 1820 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.97 % Allowed : 22.18 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.49 (0.20), residues: 1685 helix: 1.12 (0.15), residues: 1180 sheet: -0.45 (0.65), residues: 45 loop : 1.15 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 184 HIS 0.001 0.000 HIS O 62 PHE 0.041 0.001 PHE E 168 TYR 0.008 0.001 TYR E 164 ARG 0.007 0.000 ARG I 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4112.40 seconds wall clock time: 73 minutes 44.59 seconds (4424.59 seconds total)