Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 10 18:41:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5a_0670/08_2023/6j5a_0670.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5a_0670/08_2023/6j5a_0670.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5a_0670/08_2023/6j5a_0670.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5a_0670/08_2023/6j5a_0670.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5a_0670/08_2023/6j5a_0670.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5a_0670/08_2023/6j5a_0670.pdb" } resolution = 4.35 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 5542 2.51 5 N 1423 2.21 5 O 1530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "f GLU 77": "OE1" <-> "OE2" Residue "f ARG 82": "NH1" <-> "NH2" Residue "f ARG 84": "NH1" <-> "NH2" Residue "a ARG 159": "NH1" <-> "NH2" Residue "a GLU 203": "OE1" <-> "OE2" Residue "M GLU 58": "OE1" <-> "OE2" Residue "O GLU 58": "OE1" <-> "OE2" Residue "P GLU 58": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 8544 Number of models: 1 Model: "" Number of chains: 18 Chain: "b" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 440 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 5, 'TRANS': 76} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 272 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 5, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 99 Chain: "d" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 47 Chain: "e" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 315 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'TRANS': 62} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'UNK:plan-1': 63} Unresolved non-hydrogen planarities: 63 Chain: "f" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 530 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 3, 'TRANS': 83} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 112 Chain: "g" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 420 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'TRANS': 83} Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 84 Planarities with less than four sites: {'UNK:plan-1': 84} Unresolved non-hydrogen planarities: 84 Chain: "i" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 306 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 41} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "k" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 145 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'UNK:plan-1': 29} Unresolved non-hydrogen planarities: 29 Chain: "8" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 251 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "a" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1706 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 210} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "K" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "L" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "M" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "N" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 510 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 70} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "O" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "P" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "Q" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "R" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "u" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 210 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'TRANS': 41} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'UNK:plan-1': 42} Unresolved non-hydrogen planarities: 42 Time building chain proxies: 4.96, per 1000 atoms: 0.58 Number of scatterers: 8544 At special positions: 0 Unit cell: (111.78, 109.02, 113.16, 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 49 16.00 O 1530 8.00 N 1423 7.00 C 5542 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: 3.59 Conformation dependent library (CDL) restraints added in 1.3 seconds 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2326 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 0 sheets defined 89.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'b' and resid 3 through 31 Proline residue: b 18 - end of helix Proline residue: b 27 - end of helix removed outlier: 3.504A pdb=" N VAL b 31 " --> pdb=" O PRO b 27 " (cutoff:3.500A) Processing helix chain 'b' and resid 37 through 42 removed outlier: 3.917A pdb=" N LEU b 41 " --> pdb=" O LEU b 37 " (cutoff:3.500A) Processing helix chain 'b' and resid 43 through 48 Processing helix chain 'b' and resid 49 through 51 No H-bonds generated for 'chain 'b' and resid 49 through 51' Processing helix chain 'b' and resid 61 through 83 removed outlier: 4.190A pdb=" N LEU b 67 " --> pdb=" O THR b 63 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL b 68 " --> pdb=" O ILE b 64 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR b 69 " --> pdb=" O GLY b 65 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE b 70 " --> pdb=" O VAL b 66 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL b 71 " --> pdb=" O LEU b 67 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS b 72 " --> pdb=" O VAL b 68 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS b 73 " --> pdb=" O TYR b 69 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY b 75 " --> pdb=" O VAL b 71 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA b 76 " --> pdb=" O LYS b 72 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLY b 79 " --> pdb=" O GLY b 75 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA b 80 " --> pdb=" O ALA b 76 " (cutoff:3.500A) Processing helix chain 'd' and resid 133 through 137 removed outlier: 3.864A pdb=" N GLU d 137 " --> pdb=" O ASP d 134 " (cutoff:3.500A) Processing helix chain 'e' and resid 5 through 63 removed outlier: 3.501A pdb=" N UNK e 42 " --> pdb=" O UNK e 38 " (cutoff:3.500A) Processing helix chain 'f' and resid 2 through 15 removed outlier: 3.502A pdb=" N LYS f 7 " --> pdb=" O VAL f 3 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP f 8 " --> pdb=" O VAL f 4 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG f 9 " --> pdb=" O PRO f 5 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU f 11 " --> pdb=" O LYS f 7 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL f 14 " --> pdb=" O ARG f 10 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS f 15 " --> pdb=" O LEU f 11 " (cutoff:3.500A) Processing helix chain 'f' and resid 27 through 35 removed outlier: 3.749A pdb=" N GLY f 32 " --> pdb=" O PHE f 28 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE f 33 " --> pdb=" O THR f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 36 through 41 Processing helix chain 'f' and resid 42 through 44 No H-bonds generated for 'chain 'f' and resid 42 through 44' Processing helix chain 'f' and resid 55 through 60 removed outlier: 3.617A pdb=" N LEU f 59 " --> pdb=" O SER f 55 " (cutoff:3.500A) Processing helix chain 'f' and resid 61 through 75 removed outlier: 3.526A pdb=" N VAL f 67 " --> pdb=" O LEU f 63 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL f 68 " --> pdb=" O ALA f 64 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N CYS f 72 " --> pdb=" O VAL f 68 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG f 73 " --> pdb=" O PHE f 69 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER f 74 " --> pdb=" O ASN f 70 " (cutoff:3.500A) Processing helix chain 'g' and resid 2 through 32 removed outlier: 3.669A pdb=" N UNK g 7 " --> pdb=" O UNK g 3 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N UNK g 8 " --> pdb=" O UNK g 4 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N UNK g 18 " --> pdb=" O UNK g 14 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N UNK g 21 " --> pdb=" O UNK g 17 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N UNK g 25 " --> pdb=" O UNK g 21 " (cutoff:3.500A) Processing helix chain 'g' and resid 60 through 65 Processing helix chain 'g' and resid 65 through 84 removed outlier: 3.564A pdb=" N UNK g 74 " --> pdb=" O UNK g 70 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N UNK g 77 " --> pdb=" O UNK g 73 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N UNK g 78 " --> pdb=" O UNK g 74 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N UNK g 79 " --> pdb=" O UNK g 75 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N UNK g 83 " --> pdb=" O UNK g 79 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N UNK g 84 " --> pdb=" O UNK g 80 " (cutoff:3.500A) Processing helix chain 'i' and resid 14 through 26 removed outlier: 3.975A pdb=" N ASN i 19 " --> pdb=" O LYS i 15 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER i 20 " --> pdb=" O LYS i 16 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LEU i 23 " --> pdb=" O ASN i 19 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N THR i 24 " --> pdb=" O SER i 20 " (cutoff:3.500A) Processing helix chain 'i' and resid 27 through 48 removed outlier: 4.493A pdb=" N LEU i 31 " --> pdb=" O MET i 27 " (cutoff:3.500A) Processing helix chain 'k' and resid 12 through 29 removed outlier: 3.818A pdb=" N UNK k 16 " --> pdb=" O UNK k 12 " (cutoff:3.500A) Processing helix chain '8' and resid 12 through 16 removed outlier: 3.667A pdb=" N SER 8 15 " --> pdb=" O THR 8 12 " (cutoff:3.500A) Processing helix chain '8' and resid 19 through 28 removed outlier: 3.706A pdb=" N LEU 8 23 " --> pdb=" O THR 8 19 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLN 8 25 " --> pdb=" O PHE 8 21 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU 8 26 " --> pdb=" O ILE 8 22 " (cutoff:3.500A) Processing helix chain 'a' and resid 19 through 24 removed outlier: 4.165A pdb=" N ILE a 23 " --> pdb=" O ILE a 19 " (cutoff:3.500A) Processing helix chain 'a' and resid 25 through 29 Processing helix chain 'a' and resid 43 through 54 removed outlier: 3.796A pdb=" N LEU a 49 " --> pdb=" O ILE a 45 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN a 51 " --> pdb=" O GLN a 47 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR a 53 " --> pdb=" O LEU a 49 " (cutoff:3.500A) Processing helix chain 'a' and resid 68 through 73 removed outlier: 3.737A pdb=" N LEU a 72 " --> pdb=" O TRP a 68 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET a 73 " --> pdb=" O SER a 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 68 through 73' Processing helix chain 'a' and resid 73 through 82 removed outlier: 3.814A pdb=" N MET a 77 " --> pdb=" O MET a 73 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE a 79 " --> pdb=" O LEU a 75 " (cutoff:3.500A) Processing helix chain 'a' and resid 84 through 88 removed outlier: 3.820A pdb=" N LEU a 87 " --> pdb=" O ILE a 84 " (cutoff:3.500A) Processing helix chain 'a' and resid 93 through 96 Processing helix chain 'a' and resid 97 through 102 removed outlier: 4.551A pdb=" N ASN a 101 " --> pdb=" O GLN a 97 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU a 102 " --> pdb=" O LEU a 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 97 through 102' Processing helix chain 'a' and resid 105 through 117 removed outlier: 4.139A pdb=" N ALA a 111 " --> pdb=" O PRO a 107 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR a 112 " --> pdb=" O LEU a 108 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL a 113 " --> pdb=" O TRP a 109 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE a 114 " --> pdb=" O SER a 110 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR a 115 " --> pdb=" O ALA a 111 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY a 116 " --> pdb=" O THR a 112 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE a 117 " --> pdb=" O VAL a 113 " (cutoff:3.500A) Processing helix chain 'a' and resid 150 through 180 removed outlier: 4.580A pdb=" N VAL a 154 " --> pdb=" O PHE a 150 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG a 159 " --> pdb=" O ALA a 155 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU a 160 " --> pdb=" O LEU a 156 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASN a 163 " --> pdb=" O ARG a 159 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE a 164 " --> pdb=" O LEU a 160 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR a 165 " --> pdb=" O THR a 161 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA a 166 " --> pdb=" O ALA a 162 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS a 168 " --> pdb=" O ILE a 164 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU a 170 " --> pdb=" O ALA a 166 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR a 178 " --> pdb=" O ILE a 174 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU a 179 " --> pdb=" O GLY a 175 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 202 removed outlier: 4.207A pdb=" N PHE a 190 " --> pdb=" O THR a 186 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR a 200 " --> pdb=" O LEU a 196 " (cutoff:3.500A) Processing helix chain 'a' and resid 206 through 222 removed outlier: 3.834A pdb=" N GLN a 210 " --> pdb=" O VAL a 206 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA a 211 " --> pdb=" O ALA a 207 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR a 212 " --> pdb=" O LEU a 208 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N THR a 215 " --> pdb=" O ALA a 211 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU a 216 " --> pdb=" O TYR a 212 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER a 219 " --> pdb=" O THR a 215 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 15 removed outlier: 3.700A pdb=" N ILE K 9 " --> pdb=" O ALA K 5 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY K 12 " --> pdb=" O PHE K 8 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR K 15 " --> pdb=" O ALA K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 37 removed outlier: 3.958A pdb=" N GLY K 26 " --> pdb=" O GLY K 22 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR K 27 " --> pdb=" O ALA K 23 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL K 28 " --> pdb=" O GLY K 24 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE K 29 " --> pdb=" O ILE K 25 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET K 32 " --> pdb=" O VAL K 28 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE K 33 " --> pdb=" O PHE K 29 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE K 34 " --> pdb=" O GLY K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 73 removed outlier: 4.206A pdb=" N SER K 48 " --> pdb=" O GLN K 44 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER K 57 " --> pdb=" O GLY K 53 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA K 59 " --> pdb=" O ALA K 55 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET K 60 " --> pdb=" O LEU K 56 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE K 63 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N CYS K 64 " --> pdb=" O MET K 60 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU K 65 " --> pdb=" O GLY K 61 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU K 72 " --> pdb=" O ALA K 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 15 removed outlier: 3.631A pdb=" N ILE L 9 " --> pdb=" O ALA L 5 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA L 11 " --> pdb=" O LYS L 7 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA L 13 " --> pdb=" O ILE L 9 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR L 15 " --> pdb=" O ALA L 11 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 24 Processing helix chain 'L' and resid 24 through 29 removed outlier: 4.195A pdb=" N VAL L 28 " --> pdb=" O GLY L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 35 removed outlier: 3.546A pdb=" N ILE L 34 " --> pdb=" O GLY L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 73 removed outlier: 4.140A pdb=" N SER L 48 " --> pdb=" O GLN L 44 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA L 50 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER L 57 " --> pdb=" O GLY L 53 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N MET L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY L 61 " --> pdb=" O SER L 57 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE L 63 " --> pdb=" O ALA L 59 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N CYS L 64 " --> pdb=" O MET L 60 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA L 68 " --> pdb=" O CYS L 64 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU L 72 " --> pdb=" O ALA L 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 14 removed outlier: 3.536A pdb=" N LYS M 7 " --> pdb=" O ASP M 3 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY M 12 " --> pdb=" O PHE M 8 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA M 14 " --> pdb=" O GLY M 10 " (cutoff:3.500A) Processing helix chain 'M' and resid 17 through 29 removed outlier: 4.418A pdb=" N SER M 21 " --> pdb=" O GLY M 17 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA M 23 " --> pdb=" O ALA M 19 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLY M 26 " --> pdb=" O GLY M 22 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL M 28 " --> pdb=" O GLY M 24 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE M 29 " --> pdb=" O ILE M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 39 removed outlier: 3.555A pdb=" N ARG M 38 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN M 39 " --> pdb=" O GLY M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 56 removed outlier: 4.172A pdb=" N SER M 48 " --> pdb=" O GLN M 44 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA M 50 " --> pdb=" O LEU M 46 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU M 52 " --> pdb=" O SER M 48 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY M 53 " --> pdb=" O TYR M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 71 removed outlier: 3.989A pdb=" N LEU M 65 " --> pdb=" O GLY M 61 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL M 67 " --> pdb=" O PHE M 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 13 removed outlier: 3.513A pdb=" N PHE N 8 " --> pdb=" O THR N 4 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY N 10 " --> pdb=" O ALA N 6 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA N 11 " --> pdb=" O LYS N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 19 removed outlier: 3.631A pdb=" N GLY N 17 " --> pdb=" O ALA N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 37 removed outlier: 3.569A pdb=" N ILE N 25 " --> pdb=" O SER N 21 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLY N 26 " --> pdb=" O GLY N 22 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL N 28 " --> pdb=" O GLY N 24 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET N 32 " --> pdb=" O VAL N 28 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE N 33 " --> pdb=" O PHE N 29 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE N 34 " --> pdb=" O GLY N 30 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY N 35 " --> pdb=" O SER N 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 63 removed outlier: 4.086A pdb=" N SER N 48 " --> pdb=" O GLN N 44 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA N 50 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE N 51 " --> pdb=" O PHE N 47 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU N 52 " --> pdb=" O SER N 48 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY N 53 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE N 63 " --> pdb=" O ALA N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 73 removed outlier: 3.511A pdb=" N PHE N 69 " --> pdb=" O LEU N 65 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU N 70 " --> pdb=" O MET N 66 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE N 71 " --> pdb=" O VAL N 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 12 removed outlier: 3.695A pdb=" N PHE O 8 " --> pdb=" O THR O 4 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE O 9 " --> pdb=" O ALA O 5 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY O 10 " --> pdb=" O ALA O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 31 removed outlier: 3.633A pdb=" N ILE O 25 " --> pdb=" O SER O 21 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR O 27 " --> pdb=" O ALA O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 32 through 37 Processing helix chain 'O' and resid 44 through 71 removed outlier: 3.966A pdb=" N SER O 48 " --> pdb=" O GLN O 44 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA O 50 " --> pdb=" O LEU O 46 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU O 56 " --> pdb=" O LEU O 52 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N CYS O 64 " --> pdb=" O MET O 60 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU O 65 " --> pdb=" O GLY O 61 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N MET O 66 " --> pdb=" O LEU O 62 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL O 67 " --> pdb=" O PHE O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 14 removed outlier: 3.784A pdb=" N PHE P 8 " --> pdb=" O THR P 4 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE P 9 " --> pdb=" O ALA P 5 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA P 11 " --> pdb=" O LYS P 7 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY P 12 " --> pdb=" O PHE P 8 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 26 removed outlier: 3.676A pdb=" N SER P 21 " --> pdb=" O GLY P 17 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY P 24 " --> pdb=" O GLY P 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 31 Processing helix chain 'P' and resid 32 through 37 Processing helix chain 'P' and resid 44 through 73 removed outlier: 4.411A pdb=" N SER P 48 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA P 50 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER P 57 " --> pdb=" O GLY P 53 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA P 59 " --> pdb=" O ALA P 55 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE P 63 " --> pdb=" O ALA P 59 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N CYS P 64 " --> pdb=" O MET P 60 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU P 65 " --> pdb=" O GLY P 61 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU P 70 " --> pdb=" O MET P 66 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE P 71 " --> pdb=" O VAL P 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 15 removed outlier: 3.643A pdb=" N PHE Q 8 " --> pdb=" O THR Q 4 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY Q 10 " --> pdb=" O ALA Q 6 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA Q 11 " --> pdb=" O LYS Q 7 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY Q 12 " --> pdb=" O PHE Q 8 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA Q 13 " --> pdb=" O ILE Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 24 Processing helix chain 'Q' and resid 27 through 37 removed outlier: 3.952A pdb=" N MET Q 32 " --> pdb=" O VAL Q 28 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE Q 33 " --> pdb=" O PHE Q 29 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE Q 34 " --> pdb=" O GLY Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 73 removed outlier: 3.829A pdb=" N SER Q 48 " --> pdb=" O GLN Q 44 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR Q 49 " --> pdb=" O GLN Q 45 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA Q 50 " --> pdb=" O LEU Q 46 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU Q 52 " --> pdb=" O SER Q 48 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE Q 54 " --> pdb=" O ALA Q 50 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS Q 64 " --> pdb=" O MET Q 60 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA Q 68 " --> pdb=" O CYS Q 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU Q 70 " --> pdb=" O MET Q 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 16 removed outlier: 3.812A pdb=" N PHE R 8 " --> pdb=" O THR R 4 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE R 9 " --> pdb=" O ALA R 5 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY R 10 " --> pdb=" O ALA R 6 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA R 14 " --> pdb=" O GLY R 10 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR R 15 " --> pdb=" O ALA R 11 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL R 16 " --> pdb=" O GLY R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 37 removed outlier: 4.294A pdb=" N SER R 21 " --> pdb=" O GLY R 17 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY R 22 " --> pdb=" O VAL R 18 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY R 26 " --> pdb=" O GLY R 22 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR R 27 " --> pdb=" O ALA R 23 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE R 29 " --> pdb=" O ILE R 25 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE R 33 " --> pdb=" O PHE R 29 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE R 34 " --> pdb=" O GLY R 30 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA R 37 " --> pdb=" O ILE R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 73 removed outlier: 3.664A pdb=" N SER R 48 " --> pdb=" O GLN R 44 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA R 50 " --> pdb=" O LEU R 46 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA R 55 " --> pdb=" O ILE R 51 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL R 67 " --> pdb=" O PHE R 63 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA R 68 " --> pdb=" O CYS R 64 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE R 69 " --> pdb=" O LEU R 65 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU R 72 " --> pdb=" O ALA R 68 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE R 73 " --> pdb=" O PHE R 69 " (cutoff:3.500A) Processing helix chain 'u' and resid 3 through 9 removed outlier: 3.632A pdb=" N UNK u 7 " --> pdb=" O UNK u 3 " (cutoff:3.500A) Processing helix chain 'u' and resid 16 through 35 removed outlier: 4.471A pdb=" N UNK u 20 " --> pdb=" O UNK u 16 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N UNK u 21 " --> pdb=" O UNK u 17 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N UNK u 29 " --> pdb=" O UNK u 25 " (cutoff:3.500A) 451 hydrogen bonds defined for protein. 1329 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: 2.05 Time building geometry restraints manager: 3.85 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: 2698 1.34 - 1.46: 1859 1.46 - 1.58: 4020 1.58 - 1.70: 0 1.70 - 1.82: 88 Bond restraints: 8665 Sorted by residual: bond pdb=" C GLN a 152 " pdb=" N PRO a 153 " ideal model delta sigma weight residual 1.336 1.366 -0.030 1.20e-02 6.94e+03 6.41e+00 bond pdb=" CA THR b 32 " pdb=" C THR b 32 " ideal model delta sigma weight residual 1.523 1.553 -0.029 1.30e-02 5.92e+03 5.07e+00 bond pdb=" N ASN M 39 " pdb=" CA ASN M 39 " ideal model delta sigma weight residual 1.462 1.441 0.021 1.00e-02 1.00e+04 4.34e+00 bond pdb=" CB PHE a 214 " pdb=" CG PHE a 214 " ideal model delta sigma weight residual 1.502 1.454 0.048 2.30e-02 1.89e+03 4.31e+00 bond pdb=" N UNK g 38 " pdb=" CA UNK g 38 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.90e-02 2.77e+03 4.12e+00 ... (remaining 8660 not shown) Histogram of bond angle deviations from ideal: 98.53 - 106.20: 148 106.20 - 113.87: 4926 113.87 - 121.54: 4962 121.54 - 129.21: 1723 129.21 - 136.88: 28 Bond angle restraints: 11787 Sorted by residual: angle pdb=" C UNK g 37 " pdb=" N UNK g 38 " pdb=" CA UNK g 38 " ideal model delta sigma weight residual 121.70 136.88 -15.18 1.80e+00 3.09e-01 7.11e+01 angle pdb=" C SER 8 7 " pdb=" N THR 8 8 " pdb=" CA THR 8 8 " ideal model delta sigma weight residual 121.54 133.17 -11.63 1.91e+00 2.74e-01 3.71e+01 angle pdb=" N LEU a 136 " pdb=" CA LEU a 136 " pdb=" C LEU a 136 " ideal model delta sigma weight residual 113.01 119.93 -6.92 1.20e+00 6.94e-01 3.32e+01 angle pdb=" N ALA a 135 " pdb=" CA ALA a 135 " pdb=" C ALA a 135 " ideal model delta sigma weight residual 111.69 118.55 -6.86 1.23e+00 6.61e-01 3.11e+01 angle pdb=" N THR b 32 " pdb=" CA THR b 32 " pdb=" C THR b 32 " ideal model delta sigma weight residual 111.28 117.21 -5.93 1.09e+00 8.42e-01 2.96e+01 ... (remaining 11782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.31: 4272 14.31 - 28.62: 521 28.62 - 42.94: 154 42.94 - 57.25: 41 57.25 - 71.56: 6 Dihedral angle restraints: 4994 sinusoidal: 1377 harmonic: 3617 Sorted by residual: dihedral pdb=" CA THR 8 6 " pdb=" C THR 8 6 " pdb=" N SER 8 7 " pdb=" CA SER 8 7 " ideal model delta harmonic sigma weight residual -180.00 -131.76 -48.24 0 5.00e+00 4.00e-02 9.31e+01 dihedral pdb=" CA ILE f 23 " pdb=" C ILE f 23 " pdb=" N LEU f 24 " pdb=" CA LEU f 24 " ideal model delta harmonic sigma weight residual -180.00 -133.31 -46.69 0 5.00e+00 4.00e-02 8.72e+01 dihedral pdb=" CA THR 8 8 " pdb=" C THR 8 8 " pdb=" N TRP 8 9 " pdb=" CA TRP 8 9 " ideal model delta harmonic sigma weight residual 180.00 140.95 39.05 0 5.00e+00 4.00e-02 6.10e+01 ... (remaining 4991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1035 0.047 - 0.095: 316 0.095 - 0.142: 88 0.142 - 0.190: 27 0.190 - 0.237: 12 Chirality restraints: 1478 Sorted by residual: chirality pdb=" CB THR 8 8 " pdb=" CA THR 8 8 " pdb=" OG1 THR 8 8 " pdb=" CG2 THR 8 8 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB VAL L 28 " pdb=" CA VAL L 28 " pdb=" CG1 VAL L 28 " pdb=" CG2 VAL L 28 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB VAL K 18 " pdb=" CA VAL K 18 " pdb=" CG1 VAL K 18 " pdb=" CG2 VAL K 18 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1475 not shown) Planarity restraints: 1488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN O 39 " 0.062 5.00e-02 4.00e+02 9.42e-02 1.42e+01 pdb=" N PRO O 40 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO O 40 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO O 40 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU f 16 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C LEU f 16 " -0.058 2.00e-02 2.50e+03 pdb=" O LEU f 16 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY f 17 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN M 39 " -0.053 5.00e-02 4.00e+02 8.00e-02 1.02e+01 pdb=" N PRO M 40 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO M 40 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO M 40 " -0.043 5.00e-02 4.00e+02 ... (remaining 1485 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 70 2.48 - 3.09: 5633 3.09 - 3.69: 13365 3.69 - 4.30: 17885 4.30 - 4.90: 27831 Nonbonded interactions: 64784 Sorted by model distance: nonbonded pdb=" O LYS f 53 " pdb=" O ARG a 41 " model vdw 1.880 3.040 nonbonded pdb=" O UNK e 21 " pdb=" CB UNK e 25 " model vdw 1.935 2.752 nonbonded pdb=" O GLU f 13 " pdb=" N GLU f 18 " model vdw 1.956 2.520 nonbonded pdb=" O UNK e 22 " pdb=" CB UNK e 26 " model vdw 1.975 2.752 nonbonded pdb=" CA VAL f 14 " pdb=" O GLU f 18 " model vdw 2.046 3.470 ... (remaining 64779 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 'K' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = (chain 'L' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = (chain 'M' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = chain 'N' selection = (chain 'O' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = (chain 'P' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = (chain 'Q' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = (chain 'R' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) } 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 group one per residue 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: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.580 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 25.370 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5646 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 : 0.008 0.091 8665 Z= 0.499 Angle : 1.250 15.182 11787 Z= 0.730 Chirality : 0.054 0.237 1478 Planarity : 0.008 0.094 1488 Dihedral : 15.225 71.561 2668 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.88 % Favored : 90.54 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.59 % 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: -6.05 (0.19), residues: 1036 helix: -4.00 (0.12), residues: 734 sheet: None (None), residues: 0 loop : -3.38 (0.31), residues: 302 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 310 time to evaluate : 0.876 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLN i 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 314 average time/residue: 0.1673 time to fit residues: 74.3379 Evaluate side-chains 198 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 196 time to evaluate : 0.856 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0758 time to fit residues: 1.3728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.8980 chunk 93 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 62 optimal weight: 0.5980 chunk 49 optimal weight: 0.3980 chunk 96 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 39 ASN a 47 GLN a 83 ASN ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 HIS a 172 HIS a 210 GLN K 39 ASN K 45 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6023 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 8665 Z= 0.199 Angle : 0.755 7.821 11787 Z= 0.378 Chirality : 0.040 0.162 1478 Planarity : 0.005 0.060 1488 Dihedral : 6.493 45.600 1306 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.34 % Favored : 92.37 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -4.65 (0.22), residues: 1036 helix: -2.74 (0.15), residues: 770 sheet: None (None), residues: 0 loop : -3.49 (0.35), residues: 266 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 244 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 247 average time/residue: 0.1605 time to fit residues: 58.3467 Evaluate side-chains 191 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 0.808 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 46 GLN M 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6387 moved from start: 0.6009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 8665 Z= 0.251 Angle : 0.757 6.952 11787 Z= 0.379 Chirality : 0.041 0.245 1478 Planarity : 0.005 0.054 1488 Dihedral : 6.038 42.836 1306 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.92 % Favored : 91.80 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -3.86 (0.23), residues: 1036 helix: -2.04 (0.16), residues: 794 sheet: None (None), residues: 0 loop : -3.71 (0.37), residues: 242 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 234 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 236 average time/residue: 0.1497 time to fit residues: 52.3111 Evaluate side-chains 185 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 0.848 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 53 optimal weight: 0.0370 chunk 75 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 32 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6329 moved from start: 0.6492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 8665 Z= 0.169 Angle : 0.674 7.006 11787 Z= 0.327 Chirality : 0.038 0.205 1478 Planarity : 0.004 0.048 1488 Dihedral : 5.611 44.007 1306 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.43 % Favored : 92.28 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -3.01 (0.24), residues: 1036 helix: -1.45 (0.17), residues: 794 sheet: None (None), residues: 0 loop : -3.32 (0.38), residues: 242 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 231 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 232 average time/residue: 0.1653 time to fit residues: 55.5466 Evaluate side-chains 188 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 0.785 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.7980 chunk 1 optimal weight: 30.0000 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 101 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 40 optimal weight: 0.0970 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 70 ASN a 46 GLN ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.7125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 8665 Z= 0.184 Angle : 0.675 7.423 11787 Z= 0.330 Chirality : 0.039 0.266 1478 Planarity : 0.004 0.049 1488 Dihedral : 5.425 42.894 1306 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.82 % Favored : 91.89 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.25), residues: 1036 helix: -1.13 (0.18), residues: 767 sheet: None (None), residues: 0 loop : -2.61 (0.37), residues: 269 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 219 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 219 average time/residue: 0.1657 time to fit residues: 53.8357 Evaluate side-chains 187 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 0.854 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 62 optimal weight: 0.2980 chunk 114 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 70 ASN ** 8 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 46 GLN ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.7528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 8665 Z= 0.177 Angle : 0.657 7.752 11787 Z= 0.321 Chirality : 0.039 0.410 1478 Planarity : 0.004 0.050 1488 Dihedral : 5.276 41.919 1306 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.95 % Favored : 92.86 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.26), residues: 1036 helix: -0.83 (0.19), residues: 765 sheet: None (None), residues: 0 loop : -2.14 (0.40), residues: 271 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 222 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 222 average time/residue: 0.1624 time to fit residues: 52.5387 Evaluate side-chains 190 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 0.859 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 73 optimal weight: 0.0470 chunk 47 optimal weight: 1.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 70 ASN a 46 GLN ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.7855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 8665 Z= 0.160 Angle : 0.641 8.306 11787 Z= 0.309 Chirality : 0.038 0.345 1478 Planarity : 0.004 0.045 1488 Dihedral : 5.032 41.001 1306 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -1.70 (0.27), residues: 1036 helix: -0.65 (0.19), residues: 771 sheet: None (None), residues: 0 loop : -2.19 (0.40), residues: 265 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 227 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.1532 time to fit residues: 51.4348 Evaluate side-chains 188 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 0.878 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 93 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 70 ASN ** a 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.8231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 8665 Z= 0.179 Angle : 0.663 8.584 11787 Z= 0.323 Chirality : 0.039 0.321 1478 Planarity : 0.004 0.044 1488 Dihedral : 5.131 41.476 1306 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.63 % Favored : 92.28 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.56 (0.27), residues: 1036 helix: -0.57 (0.19), residues: 766 sheet: None (None), residues: 0 loop : -2.06 (0.40), residues: 270 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 213 time to evaluate : 0.822 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 213 average time/residue: 0.1565 time to fit residues: 49.5531 Evaluate side-chains 186 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 0.968 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 116 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 70 ASN ** a 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.8418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 8665 Z= 0.157 Angle : 0.662 8.578 11787 Z= 0.319 Chirality : 0.040 0.493 1478 Planarity : 0.004 0.043 1488 Dihedral : 4.919 41.419 1306 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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 (0.27), residues: 1036 helix: -0.45 (0.19), residues: 772 sheet: None (None), residues: 0 loop : -2.12 (0.41), residues: 264 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 215 time to evaluate : 0.899 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 215 average time/residue: 0.1508 time to fit residues: 48.1077 Evaluate side-chains 187 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 0.833 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 122 optimal weight: 20.0000 chunk 112 optimal weight: 0.1980 chunk 97 optimal weight: 0.5980 chunk 10 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 70 ASN ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.8618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 8665 Z= 0.165 Angle : 0.665 8.918 11787 Z= 0.318 Chirality : 0.039 0.382 1478 Planarity : 0.004 0.043 1488 Dihedral : 4.866 41.629 1306 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.25 (0.27), residues: 1036 helix: -0.33 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -1.98 (0.41), residues: 268 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 218 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 218 average time/residue: 0.1679 time to fit residues: 53.2971 Evaluate side-chains 187 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 0.849 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 97 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 0.0570 chunk 85 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 39 ASN ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.153800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.126095 restraints weight = 19780.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.127405 restraints weight = 14025.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.127791 restraints weight = 11297.160| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.8897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 8665 Z= 0.197 Angle : 0.688 8.965 11787 Z= 0.332 Chirality : 0.039 0.281 1478 Planarity : 0.004 0.045 1488 Dihedral : 5.043 41.345 1306 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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 (0.27), residues: 1036 helix: -0.32 (0.19), residues: 780 sheet: None (None), residues: 0 loop : -2.28 (0.41), residues: 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1739.37 seconds wall clock time: 32 minutes 29.25 seconds (1949.25 seconds total)