Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 10 00:20:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl2_16710/07_2023/8cl2_16710.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl2_16710/07_2023/8cl2_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_16710/07_2023/8cl2_16710.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl2_16710/07_2023/8cl2_16710.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl2_16710/07_2023/8cl2_16710.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl2_16710/07_2023/8cl2_16710.pdb" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 5.51 Conformation dependent library (CDL) restraints added in 1.9 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: 0.55 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: 3.50 Time building geometry restraints manager: 5.87 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: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 12.750 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 34.670 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.600 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 681 average time/residue: 0.2811 time to fit residues: 261.4217 Evaluate side-chains 479 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 479 time to evaluate : 1.402 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0258 ------------------------------------------------------------------------------- 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: 6.9990 chunk 69 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 129 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN A 183 ASN A 219 GLN E 192 GLN F 50 GLN I 120 HIS ** J 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 195 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: 0.7741 moved from start: 0.3269 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= 0.284 Angle : 0.635 9.619 18440 Z= 0.329 Chirality : 0.043 0.152 2085 Planarity : 0.005 0.034 2390 Dihedral : 5.185 26.405 1820 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer Outliers : 3.87 % 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: 1.17 (0.19), residues: 1685 helix: 0.75 (0.14), residues: 1170 sheet: -1.74 (0.65), residues: 45 loop : 1.59 (0.28), residues: 470 *********************** 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 594 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 539 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 32 residues processed: 572 average time/residue: 0.2822 time to fit residues: 221.6838 Evaluate side-chains 499 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 467 time to evaluate : 1.615 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.1191 time to fit residues: 9.3288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 162 optimal weight: 0.7980 chunk 133 optimal weight: 0.7980 chunk 148 optimal weight: 0.2980 chunk 51 optimal weight: 0.6980 chunk 120 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 I 120 HIS J 155 GLN ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 179 GLN L 183 ASN M 219 GLN O 179 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 13595 Z= 0.189 Angle : 0.561 9.373 18440 Z= 0.290 Chirality : 0.040 0.144 2085 Planarity : 0.005 0.035 2390 Dihedral : 4.680 20.090 1820 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer Outliers : 1.69 % 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: 1.06 (0.14), residues: 1185 sheet: -1.86 (0.67), residues: 45 loop : 1.61 (0.28), residues: 455 *********************** 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 524 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 500 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 505 average time/residue: 0.2866 time to fit residues: 199.3342 Evaluate side-chains 475 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 465 time to evaluate : 1.608 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1176 time to fit residues: 4.2832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 78 optimal weight: 0.2980 chunk 142 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 GLN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 GLN I 179 GLN I 183 ASN ** J 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 192 GLN M 219 GLN ** N 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 176 GLN O 179 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 13595 Z= 0.327 Angle : 0.614 7.557 18440 Z= 0.316 Chirality : 0.043 0.143 2085 Planarity : 0.005 0.037 2390 Dihedral : 4.712 23.299 1820 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer Outliers : 2.61 % 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: 1.31 (0.20), residues: 1685 helix: 0.93 (0.15), residues: 1185 sheet: -1.75 (0.66), residues: 45 loop : 1.40 (0.28), residues: 455 *********************** 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 494 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 457 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 26 residues processed: 467 average time/residue: 0.2821 time to fit residues: 185.0369 Evaluate side-chains 453 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 427 time to evaluate : 1.603 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1315 time to fit residues: 8.5456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 2 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 81 optimal weight: 0.0170 chunk 143 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 overall best weight: 1.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 195 ASN K 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 13595 Z= 0.237 Angle : 0.568 7.843 18440 Z= 0.294 Chirality : 0.041 0.145 2085 Planarity : 0.005 0.039 2390 Dihedral : 4.513 20.566 1820 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 1.55 % 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: 1.33 (0.20), residues: 1685 helix: 0.97 (0.15), residues: 1190 sheet: -1.54 (0.67), residues: 45 loop : 1.33 (0.29), residues: 450 *********************** 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 470 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 448 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 457 average time/residue: 0.2598 time to fit residues: 168.0478 Evaluate side-chains 423 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 413 time to evaluate : 1.477 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1195 time to fit residues: 4.2902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 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: 1.9990 chunk 83 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 F 195 ASN H 195 ASN I 179 GLN I 195 ASN ** J 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 195 ASN N 195 ASN O 183 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 13595 Z= 0.295 Angle : 0.600 11.242 18440 Z= 0.309 Chirality : 0.042 0.155 2085 Planarity : 0.005 0.039 2390 Dihedral : 4.588 19.867 1820 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer Outliers : 2.39 % 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: 1.26 (0.20), residues: 1685 helix: 0.91 (0.15), residues: 1195 sheet: -1.27 (0.65), residues: 45 loop : 1.30 (0.29), residues: 445 *********************** 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 457 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 423 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 18 residues processed: 438 average time/residue: 0.2704 time to fit residues: 166.7970 Evaluate side-chains 421 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 403 time to evaluate : 1.682 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2402 time to fit residues: 8.4762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 0.0020 chunk 17 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 73 optimal weight: 0.0980 chunk 98 optimal weight: 3.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- 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 K 195 ASN N 195 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 13595 Z= 0.174 Angle : 0.555 11.715 18440 Z= 0.287 Chirality : 0.040 0.143 2085 Planarity : 0.005 0.039 2390 Dihedral : 4.366 19.789 1820 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer Outliers : 0.70 % 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: 1.47 (0.20), residues: 1685 helix: 1.08 (0.15), residues: 1190 sheet: -0.98 (0.66), residues: 45 loop : 1.31 (0.29), residues: 450 *********************** 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 432 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 422 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 425 average time/residue: 0.2649 time to fit residues: 160.4444 Evaluate side-chains 396 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 392 time to evaluate : 1.624 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2438 time to fit residues: 3.6432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 108 optimal weight: 0.8980 chunk 78 optimal weight: 0.0170 chunk 14 optimal weight: 0.5980 chunk 125 optimal weight: 6.9990 chunk 144 optimal weight: 0.0050 overall best weight: 0.3832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN A 195 ASN E 195 ASN H 195 ASN ** J 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 195 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4969 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= 0.172 Angle : 0.588 11.212 18440 Z= 0.299 Chirality : 0.040 0.195 2085 Planarity : 0.005 0.039 2390 Dihedral : 4.319 17.905 1820 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer Outliers : 0.70 % 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: 1.09 (0.15), residues: 1190 sheet: -0.79 (0.65), residues: 45 loop : 1.22 (0.29), residues: 450 *********************** 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 426 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 416 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 420 average time/residue: 0.2627 time to fit residues: 157.3666 Evaluate side-chains 394 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 392 time to evaluate : 1.602 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1130 time to fit residues: 2.4048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 10.0000 chunk 139 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 45 optimal weight: 0.0060 chunk 133 optimal weight: 0.7980 chunk 140 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- 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 193 ASN H 195 ASN I 120 HIS K 195 ASN L 179 GLN N 195 ASN O 62 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 13595 Z= 0.222 Angle : 0.634 13.548 18440 Z= 0.321 Chirality : 0.042 0.195 2085 Planarity : 0.005 0.041 2390 Dihedral : 4.395 17.418 1820 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer Outliers : 0.70 % 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: 1.38 (0.20), residues: 1685 helix: 1.02 (0.15), residues: 1190 sheet: -0.58 (0.65), residues: 45 loop : 1.19 (0.29), residues: 450 *********************** 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 412 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 402 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 402 average time/residue: 0.2613 time to fit residues: 149.2133 Evaluate side-chains 401 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 394 time to evaluate : 1.532 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1298 time to fit residues: 3.6885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 103 optimal weight: 0.0270 overall best weight: 1.3844 ------------------------------------------------------------------------------- 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 L 179 GLN L 183 ASN N 195 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 13595 Z= 0.266 Angle : 0.657 11.525 18440 Z= 0.334 Chirality : 0.043 0.172 2085 Planarity : 0.005 0.042 2390 Dihedral : 4.485 17.867 1820 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 0.63 % 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: 1.29 (0.20), residues: 1685 helix: 0.95 (0.15), residues: 1180 sheet: -0.65 (0.64), residues: 45 loop : 1.17 (0.29), residues: 460 ********************** 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 398 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 389 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 391 average time/residue: 0.2569 time to fit residues: 142.4382 Evaluate side-chains 388 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 382 time to evaluate : 1.677 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2392 time to fit residues: 4.4795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 16 optimal weight: 0.0020 chunk 24 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.6790 ------------------------------------------------------------------------------- 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 H 195 ASN K 195 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 = 0.3781 r_free = 0.3781 target = 0.136076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.103246 restraints weight = 22430.852| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.57 r_work: 0.3188 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 13595 Z= 0.202 Angle : 0.635 11.261 18440 Z= 0.323 Chirality : 0.042 0.160 2085 Planarity : 0.005 0.042 2390 Dihedral : 4.403 18.322 1820 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 0.14 % 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: 1.32 (0.20), residues: 1685 helix: 0.94 (0.15), residues: 1185 sheet: -0.69 (0.64), residues: 45 loop : 1.28 (0.29), residues: 455 =============================================================================== Job complete usr+sys time: 3861.42 seconds wall clock time: 69 minutes 53.92 seconds (4193.92 seconds total)