Starting phenix.real_space_refine on Mon Aug 25 14:52:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qyn_18759/08_2025/8qyn_18759.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qyn_18759/08_2025/8qyn_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 { model { file = "/net/cci-nas-00/data/ceres_data/8qyn_18759/08_2025/8qyn_18759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qyn_18759/08_2025/8qyn_18759.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qyn_18759/08_2025/8qyn_18759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qyn_18759/08_2025/8qyn_18759.map" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 7.25, per 1000 atoms: 0.25 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.14 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: 6.16 Time building geometry restraints manager: 3.24 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: 0.00 - 1.23: 38871 1.23 - 2.47: 919 2.47 - 3.70: 214 3.70 - 4.94: 31 4.94 - 6.17: 9 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.010 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.320 ------------------------------------------------------------------------------- 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= 0.159 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG F 41 TYR 0.028 0.001 TYR B 121 PHE 0.025 0.001 PHE L 69 TRP 0.059 0.001 TRP F 216 HIS 0.005 0.001 HIS M 132 Details of bonding type rmsd covalent geometry : bond 0.00368 (29643) covalent geometry : angle 0.49735 (40044) hydrogen bonds : bond 0.18447 ( 1456) hydrogen bonds : angle 6.20156 ( 4164) *********************** 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 to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 1.437 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: 0.7983 (tp30) REVERT: M 162 LYS cc_start: 0.8122 (mtpt) cc_final: 0.7660 (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: 0.9174 time to fit residues: 360.0611 Evaluate side-chains 273 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 271 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 197 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 7.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 148 GLN J 229 GLN P 83 ASN Q 188 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.093952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.067254 restraints weight = 56947.088| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.75 r_work: 0.2824 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29643 Z= 0.132 Angle : 0.508 6.960 40044 Z= 0.272 Chirality : 0.042 0.170 4515 Planarity : 0.004 0.053 5137 Dihedral : 3.973 43.119 4093 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.67 % Allowed : 7.92 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.14), residues: 3663 helix: 2.78 (0.15), residues: 1311 sheet: 0.57 (0.18), residues: 840 loop : -1.04 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 222 TYR 0.019 0.001 TYR B 121 PHE 0.026 0.001 PHE A 173 TRP 0.008 0.001 TRP E 13 HIS 0.004 0.001 HIS I 125 Details of bonding type rmsd covalent geometry : bond 0.00308 (29643) covalent geometry : angle 0.50776 (40044) hydrogen bonds : bond 0.04925 ( 1456) hydrogen bonds : angle 4.54255 ( 4164) *********************** 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 to be fit. rotamer outliers: 21 poor density : 274 time to evaluate : 1.326 Fit side-chains revert: symmetry clash REVERT: B 140 ASP cc_start: 0.8310 (t0) cc_final: 0.7914 (t0) REVERT: C 23 GLN cc_start: 0.8411 (tm-30) cc_final: 0.8018 (tm-30) REVERT: C 200 GLN cc_start: 0.8018 (pp30) cc_final: 0.7534 (pp30) REVERT: D 211 ASN cc_start: 0.9274 (p0) cc_final: 0.8959 (p0) REVERT: F 207 ASP cc_start: 0.8117 (m-30) cc_final: 0.7687 (m-30) REVERT: F 222 ASN cc_start: 0.9036 (t0) cc_final: 0.8346 (t0) REVERT: G 236 ASP cc_start: 0.8571 (t70) cc_final: 0.8138 (p0) REVERT: L 116 THR cc_start: 0.8688 (t) cc_final: 0.8443 (p) REVERT: L 173 ASN cc_start: 0.8584 (m110) cc_final: 0.8046 (m110) REVERT: N 56 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7688 (mtm) REVERT: N 221 GLN cc_start: 0.7769 (mm110) cc_final: 0.7383 (mp10) outliers start: 21 outliers final: 3 residues processed: 281 average time/residue: 0.8649 time to fit residues: 277.8454 Evaluate side-chains 267 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 263 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 187 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 198 optimal weight: 10.0000 chunk 360 optimal weight: 0.9990 chunk 154 optimal weight: 6.9990 chunk 260 optimal weight: 7.9990 chunk 213 optimal weight: 0.0670 chunk 232 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 366 optimal weight: 20.0000 chunk 329 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 294 optimal weight: 5.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- 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 12 HIS G 224 ASN H 108 ASN J 148 GLN P 83 ASN Q 188 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.093184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.066472 restraints weight = 57193.808| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.74 r_work: 0.2809 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29643 Z= 0.147 Angle : 0.503 7.190 40044 Z= 0.268 Chirality : 0.042 0.167 4515 Planarity : 0.004 0.056 5137 Dihedral : 3.950 29.740 4088 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.93 % Allowed : 10.01 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.14), residues: 3663 helix: 2.76 (0.15), residues: 1314 sheet: 0.68 (0.18), residues: 825 loop : -1.07 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 41 TYR 0.023 0.001 TYR B 121 PHE 0.024 0.001 PHE L 69 TRP 0.009 0.001 TRP E 13 HIS 0.005 0.001 HIS G 12 Details of bonding type rmsd covalent geometry : bond 0.00361 (29643) covalent geometry : angle 0.50322 (40044) hydrogen bonds : bond 0.04977 ( 1456) hydrogen bonds : angle 4.29061 ( 4164) *********************** 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 300 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 271 time to evaluate : 1.345 Fit side-chains REVERT: B 140 ASP cc_start: 0.8331 (t0) cc_final: 0.7912 (t0) REVERT: C 23 GLN cc_start: 0.8472 (tm-30) cc_final: 0.8024 (tm-30) REVERT: D 211 ASN cc_start: 0.9264 (p0) cc_final: 0.8974 (p0) REVERT: E 217 LYS cc_start: 0.8603 (ttpt) cc_final: 0.8176 (tptm) REVERT: F 207 ASP cc_start: 0.8167 (m-30) cc_final: 0.7698 (m-30) REVERT: F 222 ASN cc_start: 0.9016 (t0) cc_final: 0.8283 (t0) REVERT: G 236 ASP cc_start: 0.8595 (t70) cc_final: 0.8145 (p0) REVERT: H 90 GLN cc_start: 0.8888 (mt0) cc_final: 0.8593 (mt0) REVERT: I 33 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7944 (tm-30) REVERT: L 116 THR cc_start: 0.8723 (t) cc_final: 0.8506 (p) REVERT: L 173 ASN cc_start: 0.8617 (m110) cc_final: 0.8114 (m110) REVERT: N 9 ARG cc_start: 0.8726 (tpp80) cc_final: 0.8305 (ptp-110) REVERT: N 56 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7704 (mtm) REVERT: N 221 GLN cc_start: 0.7766 (mm110) cc_final: 0.7391 (mp10) REVERT: O 229 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8345 (mp0) outliers start: 29 outliers final: 11 residues processed: 282 average time/residue: 0.8398 time to fit residues: 271.5347 Evaluate side-chains 277 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 263 time to evaluate : 1.234 ------------------------------------------------------------------------------- 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 15 VAL 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 Chi-restraints excluded: chain N residue 199 ASP Chi-restraints excluded: chain O residue 229 GLU Chi-restraints excluded: chain P residue 101 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 204 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 131 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 120 optimal weight: 0.5980 chunk 338 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- 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 N 210 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 = 0.3381 r_free = 0.3381 target = 0.092814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.066058 restraints weight = 57062.654| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.74 r_work: 0.2801 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1100 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= 0.156 Angle : 0.505 7.065 40044 Z= 0.269 Chirality : 0.043 0.167 4515 Planarity : 0.004 0.058 5137 Dihedral : 3.987 29.114 4088 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.31 % Allowed : 11.48 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.14), residues: 3663 helix: 2.72 (0.15), residues: 1316 sheet: 0.70 (0.18), residues: 822 loop : -1.09 (0.15), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 186 TYR 0.020 0.001 TYR B 121 PHE 0.024 0.001 PHE L 69 TRP 0.009 0.001 TRP E 13 HIS 0.006 0.001 HIS L 162 Details of bonding type rmsd covalent geometry : bond 0.00385 (29643) covalent geometry : angle 0.50494 (40044) hydrogen bonds : bond 0.05002 ( 1456) hydrogen bonds : angle 4.21795 ( 4164) *********************** 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 316 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 275 time to evaluate : 1.481 Fit side-chains REVERT: B 140 ASP cc_start: 0.8331 (t0) cc_final: 0.7985 (t0) REVERT: C 23 GLN cc_start: 0.8462 (tm-30) cc_final: 0.8018 (tm-30) REVERT: D 211 ASN cc_start: 0.9261 (p0) cc_final: 0.9054 (p0) REVERT: E 217 LYS cc_start: 0.8624 (ttpt) cc_final: 0.8184 (tptm) REVERT: F 207 ASP cc_start: 0.8219 (m-30) cc_final: 0.7718 (m-30) REVERT: F 222 ASN cc_start: 0.8987 (t0) cc_final: 0.8257 (t0) REVERT: G 236 ASP cc_start: 0.8597 (t70) cc_final: 0.8145 (p0) REVERT: H 90 GLN cc_start: 0.8899 (mt0) cc_final: 0.8584 (mt0) REVERT: I 33 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7941 (tm-30) REVERT: L 116 THR cc_start: 0.8724 (t) cc_final: 0.8510 (p) REVERT: L 173 ASN cc_start: 0.8592 (m110) cc_final: 0.8107 (m110) REVERT: N 56 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7710 (mtm) REVERT: N 221 GLN cc_start: 0.7767 (mm110) cc_final: 0.7401 (mp10) outliers start: 41 outliers final: 17 residues processed: 294 average time/residue: 0.7861 time to fit residues: 265.7102 Evaluate side-chains 280 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 261 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 I residue 243 ASP 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 41 optimal weight: 8.9990 chunk 345 optimal weight: 5.9990 chunk 281 optimal weight: 5.9990 chunk 211 optimal weight: 4.9990 chunk 364 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 170 optimal weight: 9.9990 chunk 221 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 N 210 GLN P 83 ASN P 230 ASN Q 41 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.090355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.063647 restraints weight = 56931.018| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.74 r_work: 0.2742 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 29643 Z= 0.225 Angle : 0.565 7.217 40044 Z= 0.301 Chirality : 0.044 0.160 4515 Planarity : 0.005 0.057 5137 Dihedral : 4.222 31.458 4088 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.64 % Allowed : 12.25 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.14), residues: 3663 helix: 2.62 (0.15), residues: 1311 sheet: 0.65 (0.18), residues: 819 loop : -1.18 (0.14), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 186 TYR 0.029 0.001 TYR B 121 PHE 0.031 0.002 PHE L 69 TRP 0.010 0.001 TRP E 13 HIS 0.007 0.001 HIS I 125 Details of bonding type rmsd covalent geometry : bond 0.00566 (29643) covalent geometry : angle 0.56541 (40044) hydrogen bonds : bond 0.06090 ( 1456) hydrogen bonds : angle 4.33380 ( 4164) *********************** 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 320 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 269 time to evaluate : 1.202 Fit side-chains REVERT: A 60 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8432 (mtp85) REVERT: B 140 ASP cc_start: 0.8410 (t0) cc_final: 0.8076 (t0) REVERT: C 23 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8021 (tm-30) REVERT: E 217 LYS cc_start: 0.8660 (ttpt) cc_final: 0.8222 (tptm) REVERT: F 207 ASP cc_start: 0.8333 (m-30) cc_final: 0.7979 (m-30) REVERT: F 222 ASN cc_start: 0.9039 (t0) cc_final: 0.8304 (t0) REVERT: G 236 ASP cc_start: 0.8632 (t70) cc_final: 0.8181 (p0) REVERT: H 90 GLN cc_start: 0.8919 (mt0) cc_final: 0.8593 (mt0) REVERT: H 138 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8655 (mt) REVERT: I 33 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7964 (tt0) REVERT: L 116 THR cc_start: 0.8736 (t) cc_final: 0.8529 (p) REVERT: L 173 ASN cc_start: 0.8578 (m110) cc_final: 0.8072 (m110) REVERT: N 56 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7731 (mtm) REVERT: N 221 GLN cc_start: 0.7788 (mm110) cc_final: 0.7491 (mm110) REVERT: O 234 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7892 (pm20) REVERT: P 172 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8895 (ptp) outliers start: 51 outliers final: 21 residues processed: 297 average time/residue: 0.7676 time to fit residues: 262.1956 Evaluate side-chains 290 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 263 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain C residue 102 VAL 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 H residue 138 LEU 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 88 MET Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 28 MET Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain M residue 150 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 180 ILE Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain O residue 234 GLU Chi-restraints excluded: chain P residue 172 MET Chi-restraints excluded: chain P residue 230 ASN Chi-restraints excluded: chain Q residue 28 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 93 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 343 optimal weight: 10.0000 chunk 176 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 192 optimal weight: 10.0000 chunk 297 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 M 174 ASN N 210 GLN P 83 ASN Q 41 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.091222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.064585 restraints weight = 56905.287| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.74 r_work: 0.2720 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1266 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= 0.168 Angle : 0.523 6.911 40044 Z= 0.280 Chirality : 0.043 0.159 4515 Planarity : 0.004 0.059 5137 Dihedral : 4.162 31.283 4088 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.25 % Allowed : 13.31 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.14), residues: 3663 helix: 2.65 (0.15), residues: 1312 sheet: 0.63 (0.18), residues: 824 loop : -1.16 (0.14), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 186 TYR 0.022 0.001 TYR P 189 PHE 0.025 0.001 PHE L 69 TRP 0.009 0.001 TRP E 13 HIS 0.005 0.001 HIS I 125 Details of bonding type rmsd covalent geometry : bond 0.00418 (29643) covalent geometry : angle 0.52317 (40044) hydrogen bonds : bond 0.05281 ( 1456) hydrogen bonds : angle 4.22178 ( 4164) *********************** 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 to be fit. rotamer outliers: 39 poor density : 272 time to evaluate : 1.123 Fit side-chains REVERT: B 140 ASP cc_start: 0.8392 (t0) cc_final: 0.7923 (t0) REVERT: C 23 GLN cc_start: 0.8334 (tm-30) cc_final: 0.7801 (tm-30) REVERT: E 217 LYS cc_start: 0.8576 (ttpt) cc_final: 0.8071 (tptm) REVERT: F 207 ASP cc_start: 0.8199 (m-30) cc_final: 0.7852 (m-30) REVERT: F 222 ASN cc_start: 0.8958 (t0) cc_final: 0.8218 (t0) REVERT: G 236 ASP cc_start: 0.8575 (t70) cc_final: 0.8077 (p0) REVERT: H 90 GLN cc_start: 0.8891 (mt0) cc_final: 0.8571 (mt0) REVERT: I 33 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7917 (tm-30) REVERT: L 116 THR cc_start: 0.8673 (t) cc_final: 0.8436 (p) REVERT: L 165 GLU cc_start: 0.8727 (pm20) cc_final: 0.8435 (pm20) REVERT: L 173 ASN cc_start: 0.8508 (m110) cc_final: 0.7993 (m110) REVERT: N 221 GLN cc_start: 0.7621 (mm110) cc_final: 0.7329 (mm110) REVERT: O 234 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7646 (pm20) outliers start: 39 outliers final: 25 residues processed: 292 average time/residue: 0.7923 time to fit residues: 265.7898 Evaluate side-chains 291 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 264 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 174 MET 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 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 K residue 236 ASN 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 20 VAL Chi-restraints excluded: chain M residue 132 HIS Chi-restraints excluded: chain M residue 148 THR 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 N residue 199 ASP Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 234 GLU Chi-restraints excluded: chain P residue 101 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 351 optimal weight: 20.0000 chunk 270 optimal weight: 9.9990 chunk 309 optimal weight: 8.9990 chunk 299 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 chunk 175 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 chunk 223 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 N 210 GLN P 83 ASN Q 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.089790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.063081 restraints weight = 57322.650| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.74 r_work: 0.2729 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1350 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= 0.259 Angle : 0.590 7.719 40044 Z= 0.313 Chirality : 0.046 0.190 4515 Planarity : 0.005 0.059 5137 Dihedral : 4.335 32.620 4088 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.60 % Allowed : 13.47 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.14), residues: 3663 helix: 2.55 (0.15), residues: 1303 sheet: 0.55 (0.18), residues: 828 loop : -1.25 (0.14), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 186 TYR 0.024 0.002 TYR B 121 PHE 0.032 0.002 PHE L 69 TRP 0.011 0.001 TRP E 13 HIS 0.007 0.001 HIS I 125 Details of bonding type rmsd covalent geometry : bond 0.00654 (29643) covalent geometry : angle 0.58984 (40044) hydrogen bonds : bond 0.06363 ( 1456) hydrogen bonds : angle 4.35149 ( 4164) *********************** 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 313 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 263 time to evaluate : 1.130 Fit side-chains REVERT: B 140 ASP cc_start: 0.8408 (t0) cc_final: 0.8093 (t0) REVERT: C 23 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8028 (tm-30) REVERT: E 217 LYS cc_start: 0.8682 (ttpt) cc_final: 0.8316 (tptt) REVERT: F 222 ASN cc_start: 0.9058 (t0) cc_final: 0.8343 (t0) REVERT: H 90 GLN cc_start: 0.8927 (mt0) cc_final: 0.8613 (mt0) REVERT: H 138 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8699 (mt) REVERT: I 33 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7952 (tt0) REVERT: L 116 THR cc_start: 0.8740 (t) cc_final: 0.8533 (p) REVERT: L 173 ASN cc_start: 0.8609 (m110) cc_final: 0.8118 (m110) REVERT: M 49 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7987 (tt0) REVERT: N 221 GLN cc_start: 0.7770 (mm110) cc_final: 0.7490 (mm110) REVERT: P 172 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8877 (ptp) outliers start: 50 outliers final: 26 residues processed: 290 average time/residue: 0.6965 time to fit residues: 232.9651 Evaluate side-chains 288 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 258 time to evaluate : 1.181 ------------------------------------------------------------------------------- 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 H residue 138 LEU 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 L residue 153 LEU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 132 HIS Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain N residue 7 LEU 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 Chi-restraints excluded: chain P residue 172 MET Chi-restraints excluded: chain P residue 201 LYS Chi-restraints excluded: chain Q residue 28 SER 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 36 optimal weight: 3.9990 chunk 171 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 319 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 330 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 305 optimal weight: 8.9990 chunk 322 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 148 GLN N 210 GLN P 83 ASN Q 41 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.094624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.068152 restraints weight = 56706.037| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.74 r_work: 0.2849 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 29643 Z= 0.097 Angle : 0.480 10.090 40044 Z= 0.258 Chirality : 0.041 0.189 4515 Planarity : 0.004 0.058 5137 Dihedral : 3.933 31.332 4088 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.90 % Allowed : 14.69 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.14), residues: 3663 helix: 2.75 (0.15), residues: 1310 sheet: 0.69 (0.18), residues: 831 loop : -1.07 (0.15), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 186 TYR 0.021 0.001 TYR P 189 PHE 0.019 0.001 PHE A 173 TRP 0.011 0.001 TRP N 114 HIS 0.009 0.001 HIS L 162 Details of bonding type rmsd covalent geometry : bond 0.00217 (29643) covalent geometry : angle 0.47983 (40044) hydrogen bonds : bond 0.03493 ( 1456) hydrogen bonds : angle 3.99298 ( 4164) *********************** 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 310 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 282 time to evaluate : 1.032 Fit side-chains REVERT: C 23 GLN cc_start: 0.8466 (tm-30) cc_final: 0.7999 (tm-30) REVERT: E 217 LYS cc_start: 0.8616 (ttpt) cc_final: 0.8247 (tptt) REVERT: F 207 ASP cc_start: 0.8159 (m-30) cc_final: 0.7666 (m-30) REVERT: F 222 ASN cc_start: 0.8993 (t0) cc_final: 0.8215 (t0) REVERT: H 90 GLN cc_start: 0.8873 (mt0) cc_final: 0.8561 (mt0) REVERT: L 116 THR cc_start: 0.8701 (t) cc_final: 0.8491 (p) REVERT: L 173 ASN cc_start: 0.8506 (m110) cc_final: 0.7988 (m110) REVERT: M 174 ASN cc_start: 0.6898 (p0) cc_final: 0.6532 (p0) REVERT: N 9 ARG cc_start: 0.8696 (tpp80) cc_final: 0.8173 (ttp80) REVERT: N 221 GLN cc_start: 0.7703 (mm110) cc_final: 0.7435 (mm110) REVERT: O 201 ARG cc_start: 0.8211 (tpp-160) cc_final: 0.7985 (tpp-160) outliers start: 28 outliers final: 15 residues processed: 295 average time/residue: 0.7510 time to fit residues: 255.1884 Evaluate side-chains 286 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 271 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 154 HIS 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 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 150 THR 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 101 ASP Chi-restraints excluded: chain Q residue 222 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 29 optimal weight: 0.4980 chunk 335 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 242 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 214 optimal weight: 10.0000 chunk 293 optimal weight: 0.6980 chunk 340 optimal weight: 5.9990 chunk 278 optimal weight: 2.9990 chunk 275 optimal weight: 0.0270 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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 B 69 ASN G 224 ASN H 108 ASN J 148 GLN P 83 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.096033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.069717 restraints weight = 56783.772| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.72 r_work: 0.2873 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 29643 Z= 0.091 Angle : 0.470 8.280 40044 Z= 0.250 Chirality : 0.041 0.162 4515 Planarity : 0.004 0.058 5137 Dihedral : 3.722 31.713 4088 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.67 % Allowed : 15.20 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.14), residues: 3663 helix: 2.86 (0.15), residues: 1310 sheet: 0.78 (0.18), residues: 825 loop : -0.95 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 186 TYR 0.024 0.001 TYR L 147 PHE 0.023 0.001 PHE O 163 TRP 0.009 0.001 TRP N 114 HIS 0.003 0.000 HIS F 121 Details of bonding type rmsd covalent geometry : bond 0.00200 (29643) covalent geometry : angle 0.47042 (40044) hydrogen bonds : bond 0.03218 ( 1456) hydrogen bonds : angle 3.84750 ( 4164) *********************** 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 307 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 286 time to evaluate : 1.242 Fit side-chains REVERT: A 140 ASN cc_start: 0.8547 (m110) cc_final: 0.8125 (m-40) REVERT: C 23 GLN cc_start: 0.8473 (tm-30) cc_final: 0.7995 (tm-30) REVERT: D 10 ARG cc_start: 0.8989 (mtt180) cc_final: 0.8770 (mmt180) REVERT: E 217 LYS cc_start: 0.8634 (ttpt) cc_final: 0.8273 (tptt) REVERT: F 207 ASP cc_start: 0.8102 (m-30) cc_final: 0.7658 (m-30) REVERT: F 222 ASN cc_start: 0.8957 (t0) cc_final: 0.8183 (t0) REVERT: L 116 THR cc_start: 0.8706 (t) cc_final: 0.8505 (p) REVERT: L 173 ASN cc_start: 0.8446 (m110) cc_final: 0.7956 (m110) REVERT: M 174 ASN cc_start: 0.6924 (p0) cc_final: 0.6571 (p0) REVERT: N 9 ARG cc_start: 0.8648 (tpp80) cc_final: 0.8102 (ttp80) REVERT: N 92 LYS cc_start: 0.6802 (mmpt) cc_final: 0.6034 (mttt) REVERT: N 221 GLN cc_start: 0.7709 (mm110) cc_final: 0.7431 (mm110) REVERT: O 201 ARG cc_start: 0.8224 (tpp-160) cc_final: 0.7933 (tpp-160) outliers start: 21 outliers final: 14 residues processed: 298 average time/residue: 0.8266 time to fit residues: 282.7616 Evaluate side-chains 288 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 274 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 154 HIS Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain I residue 101 LEU 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 N residue 73 VAL Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain O residue 111 MET Chi-restraints excluded: chain Q residue 28 SER 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 234 optimal weight: 10.0000 chunk 254 optimal weight: 0.0670 chunk 62 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 253 optimal weight: 5.9990 chunk 162 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 chunk 367 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 156 optimal weight: 10.0000 overall best weight: 1.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 ASN G 224 ASN J 148 GLN P 83 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.094425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.068062 restraints weight = 56482.592| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.74 r_work: 0.2844 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29643 Z= 0.111 Angle : 0.492 10.141 40044 Z= 0.261 Chirality : 0.041 0.169 4515 Planarity : 0.004 0.059 5137 Dihedral : 3.757 30.688 4088 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.48 % Allowed : 15.68 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.14), residues: 3663 helix: 2.89 (0.15), residues: 1311 sheet: 0.82 (0.18), residues: 824 loop : -0.93 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K 186 TYR 0.021 0.001 TYR P 189 PHE 0.027 0.001 PHE A 173 TRP 0.008 0.001 TRP I 102 HIS 0.004 0.001 HIS M 132 Details of bonding type rmsd covalent geometry : bond 0.00265 (29643) covalent geometry : angle 0.49240 (40044) hydrogen bonds : bond 0.03852 ( 1456) hydrogen bonds : angle 3.88609 ( 4164) ********************** 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 292 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 277 time to evaluate : 1.292 Fit side-chains REVERT: A 140 ASN cc_start: 0.8553 (m110) cc_final: 0.8135 (m-40) REVERT: C 23 GLN cc_start: 0.8482 (tm-30) cc_final: 0.7978 (tm-30) REVERT: D 10 ARG cc_start: 0.8998 (mtt180) cc_final: 0.8758 (mmt180) REVERT: E 217 LYS cc_start: 0.8595 (ttpt) cc_final: 0.8258 (tptt) REVERT: F 207 ASP cc_start: 0.8120 (m-30) cc_final: 0.7657 (m-30) REVERT: F 222 ASN cc_start: 0.8996 (t0) cc_final: 0.8234 (t0) REVERT: L 116 THR cc_start: 0.8711 (t) cc_final: 0.8511 (p) REVERT: L 173 ASN cc_start: 0.8440 (m110) cc_final: 0.7956 (m110) REVERT: M 174 ASN cc_start: 0.6915 (p0) cc_final: 0.6567 (p0) REVERT: N 9 ARG cc_start: 0.8643 (tpp80) cc_final: 0.8088 (ttp80) REVERT: N 41 LEU cc_start: 0.7440 (pp) cc_final: 0.7037 (mt) REVERT: N 221 GLN cc_start: 0.7734 (mm110) cc_final: 0.7455 (mm110) REVERT: O 201 ARG cc_start: 0.8234 (tpp-160) cc_final: 0.7965 (tpp-160) REVERT: P 95 MET cc_start: 0.9127 (ptt) cc_final: 0.8916 (pmm) outliers start: 15 outliers final: 13 residues processed: 285 average time/residue: 0.8534 time to fit residues: 278.3732 Evaluate side-chains 287 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 274 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 154 HIS Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain I residue 101 LEU 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 N residue 73 VAL Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain Q residue 28 SER 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 82 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 297 optimal weight: 5.9990 chunk 285 optimal weight: 9.9990 chunk 304 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 288 optimal weight: 9.9990 chunk 360 optimal weight: 5.9990 chunk 190 optimal weight: 10.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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 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 = 0.3363 r_free = 0.3363 target = 0.091416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.064838 restraints weight = 57217.286| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.75 r_work: 0.2723 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 29643 Z= 0.185 Angle : 0.551 9.522 40044 Z= 0.291 Chirality : 0.044 0.178 4515 Planarity : 0.004 0.060 5137 Dihedral : 4.023 28.687 4088 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.64 % Allowed : 15.72 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.14), residues: 3663 helix: 2.79 (0.15), residues: 1313 sheet: 0.75 (0.18), residues: 831 loop : -1.02 (0.15), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K 186 TYR 0.025 0.001 TYR L 147 PHE 0.028 0.001 PHE A 173 TRP 0.011 0.001 TRP G 101 HIS 0.007 0.001 HIS M 132 Details of bonding type rmsd covalent geometry : bond 0.00463 (29643) covalent geometry : angle 0.55087 (40044) hydrogen bonds : bond 0.05342 ( 1456) hydrogen bonds : angle 4.09529 ( 4164) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9576.76 seconds wall clock time: 163 minutes 59.85 seconds (9839.85 seconds total)