Starting phenix.real_space_refine on Sat Aug 10 09:07:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyn_18759/08_2024/8qyn_18759.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyn_18759/08_2024/8qyn_18759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyn_18759/08_2024/8qyn_18759.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyn_18759/08_2024/8qyn_18759.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyn_18759/08_2024/8qyn_18759.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyn_18759/08_2024/8qyn_18759.cif" } resolution = 2.88 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= 0.018 sd= 0.125 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 184 5.16 5 C 18477 2.51 5 N 4971 2.21 5 O 5483 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 52": "OE1" <-> "OE2" Residue "I TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 153": "NH1" <-> "NH2" Residue "O GLU 59": "OE1" <-> "OE2" Residue "O GLU 234": "OE1" <-> "OE2" Residue "Q GLU 30": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 29115 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1805 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 221} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1937 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 241} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1826 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 226} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1840 Unusual residues: {'ACE': 1} Classifications: {'peptide': 241, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'ACE_C-N': 1, 'PTRANS': 8, 'TRANS': 232} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1889 Unusual residues: {'ACE': 1} Classifications: {'peptide': 240, 'undetermined': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 10, 'TRANS': 229} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1885 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 236} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 1892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1892 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 8, 'TRANS': 234} Chain: "H" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1008 Unusual residues: {'ACE': 1} Classifications: {'peptide': 127, 'undetermined': 1} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 119} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 2180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2180 Classifications: {'peptide': 273} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 259} Chain breaks: 2 Chain: "J" Number of atoms: 1952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1952 Unusual residues: {'ACE': 1} Classifications: {'peptide': 249, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 15, 'TRANS': 233} Chain breaks: 2 Chain: "K" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1616 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 80 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1412 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 170} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "M" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1581 Unusual residues: {'ACE': 1} Classifications: {'peptide': 197, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 8, 'TRANS': 188} Chain: "N" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1651 Unusual residues: {'ACE': 1} Classifications: {'peptide': 216, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'ACE_C-N': 1, 'PTRANS': 6, 'TRANS': 209} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "O" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1509 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 190} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "P" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1537 Classifications: {'peptide': 198} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 190} Chain breaks: 1 Chain: "Q" Number of atoms: 1515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1515 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 194} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 15.47, per 1000 atoms: 0.53 Number of scatterers: 29115 At special positions: 0 Unit cell: (148.96, 143.853, 148.109, 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 184 16.00 O 5483 8.00 N 4971 7.00 C 18477 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: 10.30 Conformation dependent library (CDL) restraints added in 4.9 seconds 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6936 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 36 sheets defined 40.3% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.63 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 removed outlier: 3.794A pdb=" N TYR A 6 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A 7 " --> pdb=" O ARG A 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3 through 7' Processing helix chain 'A' and resid 19 through 30 removed outlier: 3.923A pdb=" N GLU A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 102 removed outlier: 3.805A pdb=" N VAL A 85 " --> pdb=" O PRO A 81 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A 86 " --> pdb=" O ASP A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 120 removed outlier: 3.757A pdb=" N GLU A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 123 No H-bonds generated for 'chain 'A' and resid 121 through 123' Processing helix chain 'A' and resid 166 through 177 removed outlier: 3.861A pdb=" N GLY A 170 " --> pdb=" O ASN A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 199 removed outlier: 4.107A pdb=" N SER A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 234 removed outlier: 3.542A pdb=" N ILE A 233 " --> pdb=" O TYR A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 28 through 31 Processing helix chain 'B' and resid 79 through 102 removed outlier: 3.624A pdb=" N VAL B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 121 removed outlier: 3.635A pdb=" N ILE B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 removed outlier: 3.754A pdb=" N ALA B 171 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN B 177 " --> pdb=" O SER B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 201 Processing helix chain 'B' and resid 229 through 248 removed outlier: 3.529A pdb=" N GLU B 248 " --> pdb=" O GLU B 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 25 removed outlier: 3.680A pdb=" N GLU C 20 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C 25 " --> pdb=" O TYR C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 29 Processing helix chain 'C' and resid 55 through 60 removed outlier: 3.512A pdb=" N THR C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG C 60 " --> pdb=" O ARG C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 98 removed outlier: 3.559A pdb=" N ARG C 81 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL C 83 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG C 95 " --> pdb=" O CYS C 91 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU C 96 " --> pdb=" O GLN C 92 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR C 97 " --> pdb=" O SER C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 117 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 164 through 176 removed outlier: 4.170A pdb=" N VAL C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 196 Processing helix chain 'C' and resid 221 through 234 Processing helix chain 'D' and resid 21 through 30 removed outlier: 3.621A pdb=" N GLU D 25 " --> pdb=" O LEU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 34 Processing helix chain 'D' and resid 60 through 64 Processing helix chain 'D' and resid 81 through 104 removed outlier: 3.601A pdb=" N ALA D 85 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS D 86 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR D 87 " --> pdb=" O ALA D 83 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU D 88 " --> pdb=" O ASP D 84 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP D 90 " --> pdb=" O LYS D 86 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 121 removed outlier: 3.982A pdb=" N LEU D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA D 120 " --> pdb=" O VAL D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 removed outlier: 3.654A pdb=" N GLU D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 206 Processing helix chain 'D' and resid 230 through 239 Processing helix chain 'E' and resid 19 through 26 removed outlier: 3.714A pdb=" N GLU E 23 " --> pdb=" O ILE E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 32 removed outlier: 3.511A pdb=" N LYS E 30 " --> pdb=" O GLU E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 100 Processing helix chain 'E' and resid 104 through 118 removed outlier: 4.154A pdb=" N ILE E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 121 No H-bonds generated for 'chain 'E' and resid 119 through 121' Processing helix chain 'E' and resid 165 through 175 Processing helix chain 'E' and resid 176 through 182 removed outlier: 3.661A pdb=" N PHE E 179 " --> pdb=" O MET E 176 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N MET E 180 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU E 181 " --> pdb=" O GLU E 178 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS E 182 " --> pdb=" O PHE E 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 176 through 182' Processing helix chain 'E' and resid 183 through 196 removed outlier: 3.577A pdb=" N LEU E 187 " --> pdb=" O ASN E 183 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LYS E 189 " --> pdb=" O ASN E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 199 No H-bonds generated for 'chain 'E' and resid 197 through 199' Processing helix chain 'E' and resid 225 through 228 Processing helix chain 'E' and resid 229 through 234 Processing helix chain 'F' and resid 21 through 31 removed outlier: 3.700A pdb=" N GLU F 25 " --> pdb=" O VAL F 21 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL F 31 " --> pdb=" O ALA F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 34 No H-bonds generated for 'chain 'F' and resid 32 through 34' Processing helix chain 'F' and resid 81 through 104 Processing helix chain 'F' and resid 108 through 122 Processing helix chain 'F' and resid 123 through 125 No H-bonds generated for 'chain 'F' and resid 123 through 125' Processing helix chain 'F' and resid 169 through 178 Processing helix chain 'F' and resid 179 through 180 No H-bonds generated for 'chain 'F' and resid 179 through 180' Processing helix chain 'F' and resid 181 through 185 removed outlier: 3.830A pdb=" N MET F 185 " --> pdb=" O MET F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 202 removed outlier: 4.564A pdb=" N LYS F 192 " --> pdb=" O ARG F 188 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU F 193 " --> pdb=" O ASP F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 245 removed outlier: 3.645A pdb=" N LYS F 245 " --> pdb=" O LYS F 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 31 removed outlier: 4.021A pdb=" N GLU G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 35 removed outlier: 3.822A pdb=" N GLY G 35 " --> pdb=" O ILE G 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 32 through 35' Processing helix chain 'G' and resid 62 through 66 removed outlier: 3.527A pdb=" N VAL G 66 " --> pdb=" O SER G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 106 Processing helix chain 'G' and resid 110 through 125 removed outlier: 3.821A pdb=" N VAL G 124 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TYR G 125 " --> pdb=" O ILE G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 128 No H-bonds generated for 'chain 'G' and resid 126 through 128' Processing helix chain 'G' and resid 171 through 186 Processing helix chain 'G' and resid 190 through 207 removed outlier: 3.664A pdb=" N LEU G 202 " --> pdb=" O ALA G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 244 Processing helix chain 'H' and resid 37 through 43 removed outlier: 4.311A pdb=" N LEU H 43 " --> pdb=" O LYS H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 54 Processing helix chain 'H' and resid 54 through 71 Processing helix chain 'H' and resid 73 through 87 Processing helix chain 'H' and resid 99 through 107 removed outlier: 3.537A pdb=" N ASP H 103 " --> pdb=" O ASN H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 118 removed outlier: 3.960A pdb=" N ILE H 117 " --> pdb=" O GLY H 113 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU H 118 " --> pdb=" O PHE H 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 113 through 118' Processing helix chain 'H' and resid 120 through 124 removed outlier: 3.681A pdb=" N SER H 124 " --> pdb=" O PRO H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 139 Processing helix chain 'I' and resid 17 through 22 removed outlier: 4.525A pdb=" N GLU I 21 " --> pdb=" O GLY I 17 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU I 22 " --> pdb=" O THR I 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 17 through 22' Processing helix chain 'I' and resid 32 through 45 removed outlier: 3.595A pdb=" N ARG I 45 " --> pdb=" O LEU I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 66 removed outlier: 3.603A pdb=" N TYR I 66 " --> pdb=" O LEU I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 87 Processing helix chain 'I' and resid 145 through 155 Processing helix chain 'I' and resid 173 through 175 No H-bonds generated for 'chain 'I' and resid 173 through 175' Processing helix chain 'I' and resid 180 through 184 Processing helix chain 'I' and resid 214 through 226 Processing helix chain 'I' and resid 243 through 249 Processing helix chain 'I' and resid 250 through 256 Processing helix chain 'I' and resid 265 through 278 removed outlier: 3.609A pdb=" N SER I 269 " --> pdb=" O ASN I 265 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR I 278 " --> pdb=" O LYS I 274 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 25 No H-bonds generated for 'chain 'J' and resid 23 through 25' Processing helix chain 'J' and resid 26 through 40 Processing helix chain 'J' and resid 99 through 114 removed outlier: 3.575A pdb=" N GLY J 114 " --> pdb=" O VAL J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 129 No H-bonds generated for 'chain 'J' and resid 127 through 129' Processing helix chain 'J' and resid 131 through 135 Processing helix chain 'J' and resid 148 through 159 removed outlier: 3.633A pdb=" N GLN J 152 " --> pdb=" O GLN J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 186 through 198 Processing helix chain 'J' and resid 213 through 229 removed outlier: 3.552A pdb=" N ALA J 217 " --> pdb=" O ASN J 213 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TRP J 227 " --> pdb=" O TYR J 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 33 removed outlier: 3.634A pdb=" N ALA K 27 " --> pdb=" O ALA K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 114 Processing helix chain 'K' and resid 118 through 133 removed outlier: 3.711A pdb=" N ALA K 122 " --> pdb=" O ARG K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 184 removed outlier: 3.895A pdb=" N ALA K 177 " --> pdb=" O GLY K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 204 Processing helix chain 'K' and resid 224 through 226 No H-bonds generated for 'chain 'K' and resid 224 through 226' Processing helix chain 'L' and resid 56 through 79 Processing helix chain 'L' and resid 83 through 96 Processing helix chain 'L' and resid 97 through 99 No H-bonds generated for 'chain 'L' and resid 97 through 99' Processing helix chain 'L' and resid 142 through 154 removed outlier: 3.592A pdb=" N MET L 146 " --> pdb=" O CYS L 142 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLY L 148 " --> pdb=" O GLU L 144 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N MET L 149 " --> pdb=" O GLN L 145 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 173 Processing helix chain 'M' and resid 52 through 72 Processing helix chain 'M' and resid 76 through 95 removed outlier: 3.727A pdb=" N ARG M 93 " --> pdb=" O ALA M 89 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER M 94 " --> pdb=" O ASP M 90 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG M 95 " --> pdb=" O CYS M 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 147 Processing helix chain 'M' and resid 152 through 169 removed outlier: 3.761A pdb=" N VAL M 157 " --> pdb=" O ARG M 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 1 through 7 removed outlier: 3.509A pdb=" N SER N 5 " --> pdb=" O MET N 1 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU N 7 " --> pdb=" O LEU N 3 " (cutoff:3.500A) Processing helix chain 'N' and resid 107 through 130 Processing helix chain 'N' and resid 134 through 148 removed outlier: 3.842A pdb=" N GLN N 148 " --> pdb=" O ASN N 144 " (cutoff:3.500A) Processing helix chain 'N' and resid 190 through 201 Processing helix chain 'N' and resid 207 through 223 removed outlier: 3.684A pdb=" N THR N 223 " --> pdb=" O ILE N 219 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 108 Processing helix chain 'O' and resid 112 through 126 Processing helix chain 'O' and resid 167 through 171 removed outlier: 3.544A pdb=" N SER O 170 " --> pdb=" O GLY O 167 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALA O 171 " --> pdb=" O SER O 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 167 through 171' Processing helix chain 'O' and resid 173 through 180 Processing helix chain 'O' and resid 195 through 212 removed outlier: 3.869A pdb=" N GLU O 212 " --> pdb=" O ILE O 208 " (cutoff:3.500A) Processing helix chain 'P' and resid 101 through 123 removed outlier: 3.507A pdb=" N PHE P 105 " --> pdb=" O ASP P 101 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU P 122 " --> pdb=" O ASP P 118 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY P 123 " --> pdb=" O GLU P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 129 through 147 removed outlier: 3.728A pdb=" N LYS P 147 " --> pdb=" O SER P 143 " (cutoff:3.500A) Processing helix chain 'P' and resid 187 through 202 Proline residue: P 193 - end of helix Processing helix chain 'P' and resid 206 through 225 removed outlier: 3.548A pdb=" N ASP P 225 " --> pdb=" O LEU P 221 " (cutoff:3.500A) Processing helix chain 'Q' and resid 17 through 21 removed outlier: 3.515A pdb=" N ALA Q 21 " --> pdb=" O TRP Q 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 17 through 21' Processing helix chain 'Q' and resid 25 through 29 Processing helix chain 'Q' and resid 82 through 105 Processing helix chain 'Q' and resid 109 through 124 removed outlier: 3.839A pdb=" N MET Q 120 " --> pdb=" O LEU Q 116 " (cutoff:3.500A) Processing helix chain 'Q' and resid 169 through 177 Processing helix chain 'Q' and resid 182 through 199 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 163 Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AA3, first strand: chain 'B' and resid 161 through 164 Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 67 Processing sheet with id=AA5, first strand: chain 'C' and resid 158 through 161 Processing sheet with id=AA6, first strand: chain 'C' and resid 62 through 64 removed outlier: 3.815A pdb=" N VAL C 134 " --> pdb=" O CYS C 70 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY C 135 " --> pdb=" O ARG C 143 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS C 154 " --> pdb=" O GLN C 146 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 167 through 170 removed outlier: 4.774A pdb=" N GLN D 221 " --> pdb=" O ASN D 225 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ASN D 225 " --> pdb=" O GLN D 221 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 67 through 71 removed outlier: 6.890A pdb=" N ILE D 67 " --> pdb=" O MET D 78 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N MET D 78 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLU D 69 " --> pdb=" O CYS D 76 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N CYS D 76 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE D 74 " --> pdb=" O ASP D 71 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY D 144 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP D 147 " --> pdb=" O GLY D 150 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 158 through 161 Processing sheet with id=AB1, first strand: chain 'E' and resid 63 through 67 removed outlier: 3.617A pdb=" N ILE E 72 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE E 70 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU E 132 " --> pdb=" O THR E 147 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE E 144 " --> pdb=" O CYS E 156 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 163 through 166 removed outlier: 3.999A pdb=" N GLY F 45 " --> pdb=" O CYS F 42 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY F 218 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG F 224 " --> pdb=" O GLY F 218 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 67 through 69 Processing sheet with id=AB4, first strand: chain 'G' and resid 5 through 6 removed outlier: 5.797A pdb=" N SER G 5 " --> pdb=" O VAL I 10 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'G' and resid 165 through 169 removed outlier: 6.650A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN G 53 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 69 through 73 removed outlier: 3.522A pdb=" N PHE G 70 " --> pdb=" O CYS G 78 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS G 78 " --> pdb=" O PHE G 70 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE G 141 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL G 151 " --> pdb=" O PHE G 163 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 14 through 15 removed outlier: 3.515A pdb=" N ILE H 14 " --> pdb=" O LEU N 39 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 56 through 57 removed outlier: 3.545A pdb=" N THR I 56 " --> pdb=" O ARG I 51 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE I 123 " --> pdb=" O VAL I 96 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N CYS I 98 " --> pdb=" O CYS I 121 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N CYS I 121 " --> pdb=" O CYS I 98 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL I 122 " --> pdb=" O GLN I 136 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LYS I 70 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N CYS I 135 " --> pdb=" O LYS I 70 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE I 72 " --> pdb=" O CYS I 135 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N CYS I 137 " --> pdb=" O ILE I 72 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ALA I 74 " --> pdb=" O CYS I 137 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N CYS I 169 " --> pdb=" O ILE I 75 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 212 through 213 Processing sheet with id=AC1, first strand: chain 'J' and resid 1 through 4 removed outlier: 3.524A pdb=" N SER J 42 " --> pdb=" O SER J 79 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL J 77 " --> pdb=" O ILE J 44 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TYR J 46 " --> pdb=" O ALA J 75 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ALA J 75 " --> pdb=" O TYR J 46 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N THR J 16 " --> pdb=" O VAL J 86 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU J 88 " --> pdb=" O THR J 16 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU J 18 " --> pdb=" O LEU J 88 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N LEU J 90 " --> pdb=" O LEU J 18 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU J 17 " --> pdb=" O ILE J 119 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N LEU J 121 " --> pdb=" O LEU J 17 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N MET J 19 " --> pdb=" O LEU J 121 " (cutoff:3.500A) removed outlier: 9.434A pdb=" N SER J 123 " --> pdb=" O MET J 19 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL J 118 " --> pdb=" O ALA J 202 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N LEU J 204 " --> pdb=" O VAL J 118 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL J 120 " --> pdb=" O LEU J 204 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N LYS J 206 " --> pdb=" O VAL J 120 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N SER J 122 " --> pdb=" O LYS J 206 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL J 208 " --> pdb=" O SER J 122 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N SER J 124 " --> pdb=" O VAL J 208 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 41 through 42 Processing sheet with id=AC3, first strand: chain 'K' and resid 41 through 42 removed outlier: 3.604A pdb=" N LEU K 143 " --> pdb=" O TYR K 154 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 167 through 170 removed outlier: 3.924A pdb=" N GLY K 54 " --> pdb=" O TYR K 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 256 through 259 removed outlier: 3.888A pdb=" N UNK K 256 " --> pdb=" O THR L 199 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR L 199 " --> pdb=" O UNK K 256 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE L 186 " --> pdb=" O ALA L 24 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP L 25 " --> pdb=" O ALA L 10 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA L 10 " --> pdb=" O ASP L 25 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 42 through 44 Processing sheet with id=AC7, first strand: chain 'M' and resid 129 through 132 removed outlier: 3.578A pdb=" N ILE M 183 " --> pdb=" O VAL M 13 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE M 182 " --> pdb=" O HIS M 189 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 26 through 27 removed outlier: 3.512A pdb=" N SER N 186 " --> pdb=" O GLN M 27 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL N 187 " --> pdb=" O THR N 62 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY N 70 " --> pdb=" O PHE N 67 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL N 71 " --> pdb=" O VAL N 238 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL N 73 " --> pdb=" O TYR N 236 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY N 242 " --> pdb=" O ARG N 239 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 35 through 39 removed outlier: 6.673A pdb=" N ILE M 42 " --> pdb=" O MET M 38 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU M 102 " --> pdb=" O MET M 118 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET M 118 " --> pdb=" O LEU M 102 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 18 through 19 Processing sheet with id=AD2, first strand: chain 'N' and resid 93 through 94 removed outlier: 4.049A pdb=" N MET N 159 " --> pdb=" O THR N 103 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY N 162 " --> pdb=" O GLY N 169 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 163 through 165 Processing sheet with id=AD4, first strand: chain 'O' and resid 57 through 58 Processing sheet with id=AD5, first strand: chain 'O' and resid 71 through 75 removed outlier: 6.843A pdb=" N THR O 78 " --> pdb=" O LEU O 74 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL O 149 " --> pdb=" O ASP O 161 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN O 159 " --> pdb=" O SER O 151 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 181 through 184 Processing sheet with id=AD7, first strand: chain 'P' and resid 87 through 91 removed outlier: 6.735A pdb=" N THR P 94 " --> pdb=" O VAL P 90 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 159 through 163 removed outlier: 5.111A pdb=" N THR Q 36 " --> pdb=" O ASP Q 51 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Q' and resid 69 through 70 removed outlier: 3.678A pdb=" N ASP Q 138 " --> pdb=" O GLY Q 142 " (cutoff:3.500A) 1458 hydrogen bonds defined for protein. 4164 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: 10.06 Time building geometry restraints manager: 11.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6914 1.33 - 1.45: 5744 1.45 - 1.57: 16693 1.57 - 1.69: 0 1.69 - 1.81: 292 Bond restraints: 29643 Sorted by residual: bond pdb=" N ILE M 151 " pdb=" CA ILE M 151 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.79e+00 bond pdb=" N THR M 150 " pdb=" CA THR M 150 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.16e-02 7.43e+03 6.78e+00 bond pdb=" N SER M 152 " pdb=" CA SER M 152 " ideal model delta sigma weight residual 1.455 1.486 -0.032 1.25e-02 6.40e+03 6.37e+00 bond pdb=" N GLU M 154 " pdb=" CA GLU M 154 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.18e-02 7.18e+03 6.11e+00 bond pdb=" N ARG M 153 " pdb=" CA ARG M 153 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.23e-02 6.61e+03 5.72e+00 ... (remaining 29638 not shown) Histogram of bond angle deviations from ideal: 98.70 - 105.76: 555 105.76 - 112.83: 15764 112.83 - 119.90: 9892 119.90 - 126.96: 13571 126.96 - 134.03: 262 Bond angle restraints: 40044 Sorted by residual: angle pdb=" N GLY M 133 " pdb=" CA GLY M 133 " pdb=" C GLY M 133 " ideal model delta sigma weight residual 111.21 115.28 -4.07 1.04e+00 9.25e-01 1.53e+01 angle pdb=" CA TYR M 12 " pdb=" C TYR M 12 " pdb=" O TYR M 12 " ideal model delta sigma weight residual 121.10 117.10 4.00 1.10e+00 8.26e-01 1.32e+01 angle pdb=" CA ASP M 11 " pdb=" C ASP M 11 " pdb=" O ASP M 11 " ideal model delta sigma weight residual 121.20 117.53 3.67 1.04e+00 9.25e-01 1.25e+01 angle pdb=" N GLU L 165 " pdb=" CA GLU L 165 " pdb=" CB GLU L 165 " ideal model delta sigma weight residual 110.12 114.70 -4.58 1.47e+00 4.63e-01 9.70e+00 angle pdb=" C SER F 63 " pdb=" N ASN F 64 " pdb=" CA ASN F 64 " ideal model delta sigma weight residual 121.54 127.00 -5.46 1.91e+00 2.74e-01 8.17e+00 ... (remaining 40039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 16213 17.70 - 35.39: 1404 35.39 - 53.08: 231 53.08 - 70.78: 48 70.78 - 88.47: 14 Dihedral angle restraints: 17910 sinusoidal: 7099 harmonic: 10811 Sorted by residual: dihedral pdb=" CA PHE O 130 " pdb=" C PHE O 130 " pdb=" N PRO O 131 " pdb=" CA PRO O 131 " ideal model delta harmonic sigma weight residual 180.00 -160.62 -19.38 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA ASP K 60 " pdb=" CB ASP K 60 " pdb=" CG ASP K 60 " pdb=" OD1 ASP K 60 " ideal model delta sinusoidal sigma weight residual -30.00 -87.77 57.77 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA PRO O 131 " pdb=" C PRO O 131 " pdb=" N TYR O 132 " pdb=" CA TYR O 132 " ideal model delta harmonic sigma weight residual 180.00 163.47 16.53 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 17907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3057 0.036 - 0.072: 997 0.072 - 0.108: 347 0.108 - 0.144: 110 0.144 - 0.180: 4 Chirality restraints: 4515 Sorted by residual: chirality pdb=" CA VAL M 13 " pdb=" N VAL M 13 " pdb=" C VAL M 13 " pdb=" CB VAL M 13 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.09e-01 chirality pdb=" CA ASN F 64 " pdb=" N ASN F 64 " pdb=" C ASN F 64 " pdb=" CB ASN F 64 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA PHE O 207 " pdb=" N PHE O 207 " pdb=" C PHE O 207 " pdb=" CB PHE O 207 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.72e-01 ... (remaining 4512 not shown) Planarity restraints: 5137 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 216 " -0.023 2.00e-02 2.50e+03 2.19e-02 1.20e+01 pdb=" CG TRP F 216 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP F 216 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP F 216 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 216 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 216 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP F 216 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 216 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 216 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP F 216 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 186 " 0.016 2.00e-02 2.50e+03 3.15e-02 9.91e+00 pdb=" C GLU E 186 " -0.054 2.00e-02 2.50e+03 pdb=" O GLU E 186 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU E 187 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 157 " 0.039 5.00e-02 4.00e+02 5.81e-02 5.41e+00 pdb=" N PRO D 158 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 158 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 158 " 0.032 5.00e-02 4.00e+02 ... (remaining 5134 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 6767 2.79 - 3.32: 24699 3.32 - 3.85: 44025 3.85 - 4.37: 50506 4.37 - 4.90: 94888 Nonbonded interactions: 220885 Sorted by model distance: nonbonded pdb=" OH TYR I 175 " pdb=" OE1 GLU I 207 " model vdw 2.265 3.040 nonbonded pdb=" O GLY B 165 " pdb=" OG SER B 168 " model vdw 2.273 3.040 nonbonded pdb=" OD1 ASP C 39 " pdb=" NH1 ARG C 213 " model vdw 2.278 3.120 nonbonded pdb=" OG SER C 130 " pdb=" O THR C 147 " model vdw 2.282 3.040 nonbonded pdb=" NH1 ARG E 164 " pdb=" OD2 ASP I 243 " model vdw 2.288 3.120 ... (remaining 220880 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 1.200 Check model and map are aligned: 0.210 Set scattering table: 0.290 Process input model: 72.350 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 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 0.039 29643 Z= 0.238 Angle : 0.497 6.172 40044 Z= 0.272 Chirality : 0.042 0.180 4515 Planarity : 0.004 0.058 5137 Dihedral : 13.482 88.475 10974 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % 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: 1.04 (0.14), residues: 3663 helix: 2.72 (0.15), residues: 1296 sheet: 0.39 (0.18), residues: 847 loop : -0.98 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.001 TRP F 216 HIS 0.005 0.001 HIS M 132 PHE 0.025 0.001 PHE L 69 TYR 0.028 0.001 TYR B 121 ARG 0.003 0.000 ARG F 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 3.075 Fit side-chains REVERT: B 140 ASP cc_start: 0.8082 (t0) cc_final: 0.7794 (t0) REVERT: C 200 GLN cc_start: 0.7767 (pp30) cc_final: 0.7547 (pp30) REVERT: F 207 ASP cc_start: 0.8213 (m-30) cc_final: 0.7911 (m-30) REVERT: F 222 ASN cc_start: 0.8846 (t0) cc_final: 0.8169 (t0) REVERT: G 236 ASP cc_start: 0.8313 (t70) cc_final: 0.8068 (p0) REVERT: J 32 MET cc_start: 0.8534 (mmm) cc_final: 0.8298 (mmt) REVERT: L 116 THR cc_start: 0.8705 (t) cc_final: 0.8463 (p) REVERT: L 173 ASN cc_start: 0.8423 (m110) cc_final: 0.8004 (m110) REVERT: M 1 MET cc_start: 0.7629 (ptm) cc_final: 0.7163 (ptm) REVERT: M 158 GLU cc_start: 0.8570 (tp30) cc_final: 0.7980 (tp30) REVERT: M 162 LYS cc_start: 0.8122 (mtpt) cc_final: 0.7674 (mtpp) REVERT: N 165 LYS cc_start: 0.9048 (mtmm) cc_final: 0.8787 (mtpt) REVERT: N 221 GLN cc_start: 0.7876 (mm110) cc_final: 0.7485 (mp10) outliers start: 0 outliers final: 2 residues processed: 347 average time/residue: 1.6667 time to fit residues: 659.9223 Evaluate side-chains 273 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 271 time to evaluate : 3.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 216 TRP Chi-restraints excluded: chain J residue 55 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 310 optimal weight: 1.9990 chunk 278 optimal weight: 0.9990 chunk 154 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 chunk 149 optimal weight: 0.8980 chunk 288 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 175 optimal weight: 7.9990 chunk 214 optimal weight: 10.0000 chunk 334 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN A 169 ASN G 224 ASN H 108 ASN J 148 GLN J 229 GLN P 83 ASN Q 41 GLN Q 188 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 29643 Z= 0.288 Angle : 0.541 7.209 40044 Z= 0.289 Chirality : 0.044 0.175 4515 Planarity : 0.004 0.053 5137 Dihedral : 4.117 42.269 4093 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.74 % Allowed : 8.27 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % 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: 1.02 (0.14), residues: 3663 helix: 2.71 (0.15), residues: 1310 sheet: 0.52 (0.18), residues: 832 loop : -1.11 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 13 HIS 0.006 0.001 HIS G 12 PHE 0.026 0.001 PHE A 173 TYR 0.027 0.001 TYR B 121 ARG 0.007 0.000 ARG F 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 272 time to evaluate : 3.242 Fit side-chains REVERT: B 140 ASP cc_start: 0.8119 (t0) cc_final: 0.7767 (t0) REVERT: C 23 GLN cc_start: 0.7899 (tm-30) cc_final: 0.7564 (tm-30) REVERT: C 200 GLN cc_start: 0.7820 (pp30) cc_final: 0.7387 (pp30) REVERT: D 211 ASN cc_start: 0.9178 (p0) cc_final: 0.8876 (p0) REVERT: F 207 ASP cc_start: 0.8280 (m-30) cc_final: 0.7946 (m-30) REVERT: F 222 ASN cc_start: 0.8865 (t0) cc_final: 0.8101 (t0) REVERT: G 236 ASP cc_start: 0.8365 (t70) cc_final: 0.8083 (p0) REVERT: H 90 GLN cc_start: 0.8516 (mt0) cc_final: 0.8242 (mt0) REVERT: I 243 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7847 (t0) REVERT: L 116 THR cc_start: 0.8720 (t) cc_final: 0.8481 (p) REVERT: L 173 ASN cc_start: 0.8563 (m110) cc_final: 0.8042 (m110) REVERT: N 56 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7646 (mtm) REVERT: N 221 GLN cc_start: 0.7901 (mm110) cc_final: 0.7516 (mp10) outliers start: 23 outliers final: 6 residues processed: 279 average time/residue: 1.5601 time to fit residues: 501.9065 Evaluate side-chains 270 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 262 time to evaluate : 3.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain I residue 243 ASP Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain N residue 56 MET Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 187 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 185 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 278 optimal weight: 2.9990 chunk 227 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 334 optimal weight: 10.0000 chunk 361 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 chunk 331 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 268 optimal weight: 9.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 12 HIS G 224 ASN J 148 GLN P 83 ASN Q 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29643 Z= 0.203 Angle : 0.496 8.277 40044 Z= 0.265 Chirality : 0.042 0.171 4515 Planarity : 0.004 0.058 5137 Dihedral : 3.959 29.354 4088 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.87 % Allowed : 10.52 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % 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: 1.12 (0.14), residues: 3663 helix: 2.76 (0.15), residues: 1308 sheet: 0.67 (0.18), residues: 829 loop : -1.07 (0.15), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 13 HIS 0.004 0.001 HIS G 12 PHE 0.024 0.001 PHE A 173 TYR 0.023 0.001 TYR P 189 ARG 0.005 0.000 ARG N 9 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 277 time to evaluate : 3.173 Fit side-chains REVERT: B 140 ASP cc_start: 0.8062 (t0) cc_final: 0.7679 (t0) REVERT: C 23 GLN cc_start: 0.7933 (tm-30) cc_final: 0.7539 (tm-30) REVERT: D 211 ASN cc_start: 0.9159 (p0) cc_final: 0.8844 (p0) REVERT: E 217 LYS cc_start: 0.8473 (ttpt) cc_final: 0.8214 (tptm) REVERT: F 207 ASP cc_start: 0.8277 (m-30) cc_final: 0.7913 (m-30) REVERT: F 222 ASN cc_start: 0.8835 (t0) cc_final: 0.8043 (t0) REVERT: G 236 ASP cc_start: 0.8350 (t70) cc_final: 0.8079 (p0) REVERT: H 90 GLN cc_start: 0.8549 (mt0) cc_final: 0.8239 (mt0) REVERT: I 33 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7890 (tm-30) REVERT: L 116 THR cc_start: 0.8773 (t) cc_final: 0.8552 (p) REVERT: L 173 ASN cc_start: 0.8581 (m110) cc_final: 0.8099 (m110) REVERT: N 9 ARG cc_start: 0.8343 (tpp80) cc_final: 0.8052 (ptp-110) REVERT: N 56 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7650 (mtm) REVERT: N 221 GLN cc_start: 0.7882 (mm110) cc_final: 0.7525 (mp10) REVERT: P 95 MET cc_start: 0.8845 (ptt) cc_final: 0.8530 (ptt) REVERT: P 212 ASP cc_start: 0.8717 (m-30) cc_final: 0.8513 (m-30) outliers start: 27 outliers final: 9 residues processed: 288 average time/residue: 1.5639 time to fit residues: 519.0423 Evaluate side-chains 273 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 262 time to evaluate : 3.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain N residue 56 MET Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 199 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 330 optimal weight: 8.9990 chunk 251 optimal weight: 40.0000 chunk 173 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 224 optimal weight: 2.9990 chunk 335 optimal weight: 6.9990 chunk 355 optimal weight: 10.0000 chunk 175 optimal weight: 0.5980 chunk 318 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 224 ASN H 108 ASN J 229 GLN P 83 ASN Q 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 29643 Z= 0.267 Angle : 0.513 7.057 40044 Z= 0.274 Chirality : 0.043 0.167 4515 Planarity : 0.004 0.058 5137 Dihedral : 4.023 29.921 4088 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.09 % Allowed : 11.80 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % 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: 1.07 (0.14), residues: 3663 helix: 2.67 (0.15), residues: 1316 sheet: 0.70 (0.18), residues: 822 loop : -1.12 (0.15), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 13 HIS 0.005 0.001 HIS I 125 PHE 0.025 0.001 PHE L 69 TYR 0.021 0.001 TYR B 121 ARG 0.005 0.000 ARG K 186 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 277 time to evaluate : 3.430 Fit side-chains REVERT: B 140 ASP cc_start: 0.8084 (t0) cc_final: 0.7756 (t0) REVERT: C 23 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7540 (tm-30) REVERT: D 211 ASN cc_start: 0.9166 (p0) cc_final: 0.8935 (p0) REVERT: E 217 LYS cc_start: 0.8491 (ttpt) cc_final: 0.8207 (tptm) REVERT: F 207 ASP cc_start: 0.8334 (m-30) cc_final: 0.7916 (m-30) REVERT: F 222 ASN cc_start: 0.8826 (t0) cc_final: 0.8043 (t0) REVERT: G 236 ASP cc_start: 0.8368 (t70) cc_final: 0.8081 (p0) REVERT: I 33 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7881 (tm-30) REVERT: L 116 THR cc_start: 0.8729 (t) cc_final: 0.8525 (p) REVERT: L 173 ASN cc_start: 0.8548 (m110) cc_final: 0.8078 (m110) REVERT: N 56 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7657 (mtm) REVERT: N 221 GLN cc_start: 0.7877 (mm110) cc_final: 0.7504 (mp10) REVERT: P 212 ASP cc_start: 0.8732 (m-30) cc_final: 0.8501 (m-30) outliers start: 34 outliers final: 16 residues processed: 292 average time/residue: 1.5443 time to fit residues: 521.7269 Evaluate side-chains 280 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 262 time to evaluate : 3.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain L residue 88 MET Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain N residue 56 MET Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain O residue 172 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 296 optimal weight: 4.9990 chunk 201 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 264 optimal weight: 8.9990 chunk 146 optimal weight: 7.9990 chunk 303 optimal weight: 0.0050 chunk 245 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 181 optimal weight: 0.7980 chunk 319 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 overall best weight: 3.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 224 ASN H 108 ASN P 83 ASN Q 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 29643 Z= 0.255 Angle : 0.509 7.011 40044 Z= 0.272 Chirality : 0.043 0.151 4515 Planarity : 0.004 0.058 5137 Dihedral : 4.037 30.171 4088 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.35 % Allowed : 12.60 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % 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: 1.07 (0.14), residues: 3663 helix: 2.68 (0.15), residues: 1316 sheet: 0.68 (0.18), residues: 826 loop : -1.12 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 13 HIS 0.005 0.001 HIS D 99 PHE 0.024 0.001 PHE L 69 TYR 0.022 0.001 TYR P 189 ARG 0.007 0.000 ARG K 186 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 271 time to evaluate : 3.261 Fit side-chains REVERT: A 60 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7938 (mtp85) REVERT: B 140 ASP cc_start: 0.8070 (t0) cc_final: 0.7773 (t0) REVERT: C 23 GLN cc_start: 0.7941 (tm-30) cc_final: 0.7520 (tm-30) REVERT: D 211 ASN cc_start: 0.9154 (p0) cc_final: 0.8930 (p0) REVERT: E 217 LYS cc_start: 0.8474 (ttpt) cc_final: 0.8187 (tptm) REVERT: F 207 ASP cc_start: 0.8342 (m-30) cc_final: 0.7919 (m-30) REVERT: F 222 ASN cc_start: 0.8823 (t0) cc_final: 0.8022 (t0) REVERT: G 236 ASP cc_start: 0.8366 (t70) cc_final: 0.8081 (p0) REVERT: H 90 GLN cc_start: 0.8558 (mt0) cc_final: 0.8265 (mt0) REVERT: I 33 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7893 (tm-30) REVERT: L 116 THR cc_start: 0.8726 (t) cc_final: 0.8523 (p) REVERT: L 173 ASN cc_start: 0.8515 (m110) cc_final: 0.8016 (m110) REVERT: N 56 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7650 (mtm) REVERT: N 221 GLN cc_start: 0.7866 (mm110) cc_final: 0.7577 (mm110) REVERT: O 234 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7842 (pm20) REVERT: P 212 ASP cc_start: 0.8754 (m-30) cc_final: 0.8513 (m-30) outliers start: 42 outliers final: 17 residues processed: 293 average time/residue: 1.5302 time to fit residues: 519.8684 Evaluate side-chains 281 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 260 time to evaluate : 3.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain I residue 243 ASP Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain K residue 236 ASN Chi-restraints excluded: chain L residue 88 MET Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain N residue 56 MET Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain O residue 234 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 119 optimal weight: 1.9990 chunk 320 optimal weight: 0.6980 chunk 70 optimal weight: 0.2980 chunk 208 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 356 optimal weight: 6.9990 chunk 295 optimal weight: 9.9990 chunk 164 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 186 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 GLN G 224 ASN H 108 ASN J 229 GLN P 83 ASN P 230 ASN Q 41 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 29643 Z= 0.158 Angle : 0.470 7.975 40044 Z= 0.251 Chirality : 0.041 0.156 4515 Planarity : 0.004 0.057 5137 Dihedral : 3.864 30.516 4088 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.03 % Allowed : 13.31 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % 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: 1.22 (0.14), residues: 3663 helix: 2.80 (0.15), residues: 1310 sheet: 0.77 (0.18), residues: 831 loop : -1.02 (0.15), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 102 HIS 0.003 0.001 HIS F 121 PHE 0.017 0.001 PHE L 69 TYR 0.022 0.001 TYR P 189 ARG 0.007 0.000 ARG K 186 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 279 time to evaluate : 3.280 Fit side-chains REVERT: B 140 ASP cc_start: 0.7952 (t0) cc_final: 0.7685 (t0) REVERT: C 23 GLN cc_start: 0.7967 (tm-30) cc_final: 0.7587 (tm-30) REVERT: D 211 ASN cc_start: 0.9110 (p0) cc_final: 0.8892 (p0) REVERT: E 217 LYS cc_start: 0.8430 (ttpt) cc_final: 0.8160 (tptm) REVERT: F 207 ASP cc_start: 0.8245 (m-30) cc_final: 0.7856 (m-30) REVERT: F 222 ASN cc_start: 0.8817 (t0) cc_final: 0.8005 (t0) REVERT: G 236 ASP cc_start: 0.8316 (t70) cc_final: 0.8062 (p0) REVERT: I 33 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7875 (tm-30) REVERT: L 173 ASN cc_start: 0.8443 (m110) cc_final: 0.7941 (m110) REVERT: N 9 ARG cc_start: 0.8281 (tpp80) cc_final: 0.7906 (ttp80) REVERT: N 56 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7657 (mtm) REVERT: N 221 GLN cc_start: 0.7864 (mm110) cc_final: 0.7563 (mm110) REVERT: O 201 ARG cc_start: 0.8119 (tpp-160) cc_final: 0.7901 (tpp-160) REVERT: O 234 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7812 (pm20) REVERT: P 172 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8553 (ptp) REVERT: P 212 ASP cc_start: 0.8786 (m-30) cc_final: 0.8544 (m-30) outliers start: 32 outliers final: 16 residues processed: 295 average time/residue: 1.5300 time to fit residues: 523.1858 Evaluate side-chains 287 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 267 time to evaluate : 3.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 154 HIS Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain L residue 88 MET Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 56 MET Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain O residue 234 GLU Chi-restraints excluded: chain P residue 101 ASP Chi-restraints excluded: chain P residue 172 MET Chi-restraints excluded: chain P residue 230 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 343 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 202 optimal weight: 6.9990 chunk 260 optimal weight: 7.9990 chunk 201 optimal weight: 5.9990 chunk 299 optimal weight: 3.9990 chunk 198 optimal weight: 9.9990 chunk 354 optimal weight: 9.9990 chunk 221 optimal weight: 4.9990 chunk 216 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 GLN G 224 ASN H 108 ASN P 83 ASN P 230 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 29643 Z= 0.435 Angle : 0.600 7.623 40044 Z= 0.318 Chirality : 0.046 0.188 4515 Planarity : 0.005 0.059 5137 Dihedral : 4.284 30.938 4088 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.35 % Allowed : 13.69 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % 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: 0.91 (0.14), residues: 3663 helix: 2.56 (0.15), residues: 1309 sheet: 0.54 (0.18), residues: 846 loop : -1.19 (0.15), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 101 HIS 0.009 0.001 HIS M 132 PHE 0.034 0.002 PHE L 69 TYR 0.026 0.002 TYR B 121 ARG 0.009 0.000 ARG K 186 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 264 time to evaluate : 3.322 Fit side-chains REVERT: A 166 ASN cc_start: 0.9030 (t0) cc_final: 0.8604 (t0) REVERT: B 140 ASP cc_start: 0.8202 (t0) cc_final: 0.7867 (t0) REVERT: C 23 GLN cc_start: 0.7985 (tm-30) cc_final: 0.7471 (tm-30) REVERT: D 211 ASN cc_start: 0.9158 (p0) cc_final: 0.8948 (p0) REVERT: F 222 ASN cc_start: 0.8889 (t0) cc_final: 0.8131 (t0) REVERT: H 90 GLN cc_start: 0.8588 (mt0) cc_final: 0.8280 (mt0) REVERT: I 33 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7890 (tm-30) REVERT: L 173 ASN cc_start: 0.8488 (m110) cc_final: 0.8003 (m110) REVERT: M 49 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7419 (tt0) REVERT: N 56 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7641 (mtm) REVERT: N 221 GLN cc_start: 0.7882 (mm110) cc_final: 0.7596 (mm110) REVERT: P 172 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8599 (ptp) REVERT: P 212 ASP cc_start: 0.8746 (m-30) cc_final: 0.8518 (m-30) outliers start: 42 outliers final: 23 residues processed: 289 average time/residue: 1.5874 time to fit residues: 529.6942 Evaluate side-chains 286 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 259 time to evaluate : 3.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 154 HIS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain L residue 14 MET Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 88 MET Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 56 MET Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 199 ASP Chi-restraints excluded: chain O residue 172 MET Chi-restraints excluded: chain P residue 172 MET Chi-restraints excluded: chain Q residue 222 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 219 optimal weight: 8.9990 chunk 141 optimal weight: 1.9990 chunk 211 optimal weight: 0.0270 chunk 106 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 225 optimal weight: 1.9990 chunk 241 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 278 optimal weight: 6.9990 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 GLN G 224 ASN H 108 ASN M 174 ASN P 83 ASN Q 41 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 29643 Z= 0.151 Angle : 0.484 7.241 40044 Z= 0.259 Chirality : 0.041 0.172 4515 Planarity : 0.004 0.059 5137 Dihedral : 3.937 30.661 4088 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.03 % Allowed : 14.37 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % 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: 1.16 (0.14), residues: 3663 helix: 2.79 (0.15), residues: 1309 sheet: 0.70 (0.18), residues: 834 loop : -1.06 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 114 HIS 0.004 0.001 HIS M 132 PHE 0.021 0.001 PHE A 173 TYR 0.013 0.001 TYR K 51 ARG 0.011 0.000 ARG K 186 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 273 time to evaluate : 3.095 Fit side-chains REVERT: A 140 ASN cc_start: 0.8366 (m110) cc_final: 0.7998 (m-40) REVERT: C 23 GLN cc_start: 0.7967 (tm-30) cc_final: 0.7564 (tm-30) REVERT: D 211 ASN cc_start: 0.9117 (p0) cc_final: 0.8895 (p0) REVERT: F 207 ASP cc_start: 0.8266 (m-30) cc_final: 0.7862 (m-30) REVERT: F 222 ASN cc_start: 0.8823 (t0) cc_final: 0.8001 (t0) REVERT: H 90 GLN cc_start: 0.8546 (mt0) cc_final: 0.8226 (mt0) REVERT: I 33 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7872 (tm-30) REVERT: L 158 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8580 (mtm) REVERT: L 165 GLU cc_start: 0.8645 (pm20) cc_final: 0.8324 (pm20) REVERT: L 173 ASN cc_start: 0.8427 (m110) cc_final: 0.7958 (m110) REVERT: N 56 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7627 (mtm) REVERT: N 221 GLN cc_start: 0.7861 (mm110) cc_final: 0.7600 (mm110) REVERT: P 172 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8547 (ptp) REVERT: P 212 ASP cc_start: 0.8821 (m-30) cc_final: 0.8588 (m-30) REVERT: P 240 LYS cc_start: 0.8701 (mppt) cc_final: 0.8355 (mmpt) REVERT: Q 224 LEU cc_start: 0.7988 (tp) cc_final: 0.7749 (pt) outliers start: 32 outliers final: 17 residues processed: 291 average time/residue: 1.4745 time to fit residues: 498.8212 Evaluate side-chains 288 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 267 time to evaluate : 3.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 154 HIS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain I residue 243 ASP Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 88 MET Chi-restraints excluded: chain L residue 158 MET Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain N residue 56 MET Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain P residue 172 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 322 optimal weight: 1.9990 chunk 339 optimal weight: 9.9990 chunk 310 optimal weight: 0.3980 chunk 330 optimal weight: 0.8980 chunk 198 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 298 optimal weight: 8.9990 chunk 312 optimal weight: 20.0000 chunk 329 optimal weight: 20.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 224 ASN J 148 GLN P 83 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 29643 Z= 0.157 Angle : 0.480 7.614 40044 Z= 0.255 Chirality : 0.041 0.165 4515 Planarity : 0.004 0.059 5137 Dihedral : 3.816 30.624 4088 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.99 % Allowed : 14.62 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % 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: 1.25 (0.14), residues: 3663 helix: 2.84 (0.15), residues: 1310 sheet: 0.76 (0.18), residues: 833 loop : -0.99 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 102 HIS 0.005 0.001 HIS M 132 PHE 0.023 0.001 PHE O 163 TYR 0.024 0.001 TYR L 147 ARG 0.012 0.000 ARG K 186 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 278 time to evaluate : 3.303 Fit side-chains REVERT: A 140 ASN cc_start: 0.8345 (m110) cc_final: 0.7971 (m-40) REVERT: C 23 GLN cc_start: 0.7980 (tm-30) cc_final: 0.7574 (tm-30) REVERT: D 1 MET cc_start: 0.8736 (mmm) cc_final: 0.8481 (mmt) REVERT: D 211 ASN cc_start: 0.9123 (p0) cc_final: 0.8890 (p0) REVERT: E 217 LYS cc_start: 0.8431 (ttpt) cc_final: 0.8069 (tptm) REVERT: F 207 ASP cc_start: 0.8233 (m-30) cc_final: 0.7856 (m-30) REVERT: F 222 ASN cc_start: 0.8821 (t0) cc_final: 0.7996 (t0) REVERT: I 33 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7868 (tm-30) REVERT: L 165 GLU cc_start: 0.8590 (pm20) cc_final: 0.8342 (pm20) REVERT: L 173 ASN cc_start: 0.8385 (m110) cc_final: 0.7910 (m110) REVERT: N 9 ARG cc_start: 0.8335 (tpp80) cc_final: 0.7854 (ttp80) REVERT: N 56 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7623 (mtm) REVERT: N 92 LYS cc_start: 0.6809 (mmpt) cc_final: 0.6174 (mttt) REVERT: N 221 GLN cc_start: 0.7860 (mm110) cc_final: 0.7563 (mm110) REVERT: P 172 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8479 (ptp) REVERT: P 212 ASP cc_start: 0.8793 (m-30) cc_final: 0.8557 (m-30) REVERT: P 240 LYS cc_start: 0.8705 (mppt) cc_final: 0.8386 (mmpt) outliers start: 31 outliers final: 19 residues processed: 293 average time/residue: 1.5226 time to fit residues: 518.6843 Evaluate side-chains 291 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 269 time to evaluate : 3.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 154 HIS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 88 MET Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain N residue 56 MET Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain O residue 111 MET Chi-restraints excluded: chain O residue 172 MET Chi-restraints excluded: chain P residue 172 MET Chi-restraints excluded: chain Q residue 222 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 217 optimal weight: 5.9990 chunk 349 optimal weight: 0.0270 chunk 213 optimal weight: 6.9990 chunk 165 optimal weight: 6.9990 chunk 242 optimal weight: 9.9990 chunk 366 optimal weight: 30.0000 chunk 337 optimal weight: 0.9990 chunk 291 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 225 optimal weight: 0.9980 chunk 179 optimal weight: 9.9990 overall best weight: 3.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 ASN B 109 GLN F 171 GLN G 224 ASN J 148 GLN P 83 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29643 Z= 0.248 Angle : 0.523 10.900 40044 Z= 0.277 Chirality : 0.043 0.176 4515 Planarity : 0.004 0.060 5137 Dihedral : 3.963 29.179 4088 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.87 % Allowed : 14.98 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % 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: 1.18 (0.14), residues: 3663 helix: 2.78 (0.15), residues: 1313 sheet: 0.71 (0.18), residues: 832 loop : -1.04 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 13 HIS 0.006 0.001 HIS M 132 PHE 0.024 0.001 PHE L 69 TYR 0.020 0.001 TYR P 189 ARG 0.013 0.000 ARG K 186 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 271 time to evaluate : 3.570 Fit side-chains revert: symmetry clash REVERT: A 140 ASN cc_start: 0.8372 (m110) cc_final: 0.7991 (m-40) REVERT: A 166 ASN cc_start: 0.9003 (t0) cc_final: 0.8595 (t0) REVERT: B 140 ASP cc_start: 0.7951 (t0) cc_final: 0.7660 (t0) REVERT: C 23 GLN cc_start: 0.7956 (tm-30) cc_final: 0.7527 (tm-30) REVERT: E 217 LYS cc_start: 0.8448 (ttpt) cc_final: 0.8069 (tptm) REVERT: F 207 ASP cc_start: 0.8303 (m-30) cc_final: 0.7890 (m-30) REVERT: F 222 ASN cc_start: 0.8857 (t0) cc_final: 0.8064 (t0) REVERT: H 90 GLN cc_start: 0.8552 (mt0) cc_final: 0.8238 (mt0) REVERT: I 33 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7877 (tm-30) REVERT: L 173 ASN cc_start: 0.8387 (m110) cc_final: 0.7928 (m110) REVERT: M 174 ASN cc_start: 0.7084 (p0) cc_final: 0.6738 (p0) REVERT: N 56 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7643 (mtm) REVERT: N 221 GLN cc_start: 0.7869 (mm110) cc_final: 0.7564 (mm110) REVERT: P 172 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8476 (ptp) REVERT: P 212 ASP cc_start: 0.8747 (m-30) cc_final: 0.8501 (m-30) REVERT: P 240 LYS cc_start: 0.8718 (mppt) cc_final: 0.8386 (mmpt) outliers start: 27 outliers final: 18 residues processed: 285 average time/residue: 1.5027 time to fit residues: 495.9165 Evaluate side-chains 289 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 268 time to evaluate : 3.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 154 HIS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 47 CYS Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 88 MET Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain N residue 56 MET Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain O residue 172 MET Chi-restraints excluded: chain P residue 172 MET Chi-restraints excluded: chain Q residue 222 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 231 optimal weight: 5.9990 chunk 310 optimal weight: 0.0980 chunk 89 optimal weight: 7.9990 chunk 269 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 292 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 300 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 ASN F 171 GLN G 224 ASN J 148 GLN P 83 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.093708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.067133 restraints weight = 56866.140| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.73 r_work: 0.2827 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29643 Z= 0.184 Angle : 0.498 9.382 40044 Z= 0.264 Chirality : 0.042 0.171 4515 Planarity : 0.004 0.061 5137 Dihedral : 3.893 29.932 4088 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.96 % Allowed : 15.07 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % 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: 1.25 (0.14), residues: 3663 helix: 2.83 (0.15), residues: 1310 sheet: 0.75 (0.18), residues: 831 loop : -0.98 (0.15), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 102 HIS 0.005 0.001 HIS M 132 PHE 0.023 0.001 PHE O 163 TYR 0.024 0.001 TYR L 147 ARG 0.013 0.000 ARG K 186 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9059.66 seconds wall clock time: 159 minutes 51.81 seconds (9591.81 seconds total)