Starting phenix.real_space_refine on Thu Aug 8 20:35:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qz9_18773/08_2024/8qz9_18773.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qz9_18773/08_2024/8qz9_18773.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qz9_18773/08_2024/8qz9_18773.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qz9_18773/08_2024/8qz9_18773.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qz9_18773/08_2024/8qz9_18773.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qz9_18773/08_2024/8qz9_18773.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 sd= 0.117 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 150 5.16 5 C 15425 2.51 5 N 4129 2.21 5 O 4513 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 205": "OE1" <-> "OE2" Residue "E GLU 173": "OE1" <-> "OE2" Residue "G PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 214": "OE1" <-> "OE2" Residue "H GLU 49": "OE1" <-> "OE2" Residue "H GLU 125": "OE1" <-> "OE2" Residue "I PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 21": "OE1" <-> "OE2" Residue "I TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 191": "OE1" <-> "OE2" Residue "K GLU 200": "OE1" <-> "OE2" Residue "L GLU 75": "OE1" <-> "OE2" Residue "M GLU 2": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 24217 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1731 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1786 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 236} Chain breaks: 1 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 84 Chain: "C" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1780 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 6, 'TRANS': 228} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1758 Unusual residues: {'ACE': 1} Classifications: {'peptide': 235, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'ACE_C-N': 1, 'PTRANS': 8, 'TRANS': 226} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1852 Unusual residues: {'ACE': 1} Classifications: {'peptide': 239, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'ACE_C-N': 1, 'PTRANS': 9, 'TRANS': 229} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 1834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1834 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1819 Unusual residues: {'ACE': 1} Classifications: {'peptide': 241, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'ACE_C-N': 1, 'PTRANS': 8, 'TRANS': 232} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "H" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 901 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 106} 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: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2056 Classifications: {'peptide': 269} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 255} Chain breaks: 2 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "J" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1888 Unusual residues: {'ACE': 1} Classifications: {'peptide': 248, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'ACE_C-N': 1, 'PTRANS': 15, 'TRANS': 232} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "K" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1566 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 11, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 41 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: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1343 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "M" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1462 Unusual residues: {'ACE': 1} Classifications: {'peptide': 196, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 188} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 79 Chain: "N" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1250 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 169} Chain breaks: 3 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 76 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 72 Chain: "O" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1111 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain breaks: 4 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 6, 'TYR:plan': 1, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 84 Time building chain proxies: 13.66, per 1000 atoms: 0.56 Number of scatterers: 24217 At special positions: 0 Unit cell: (146.406, 141.299, 146.406, 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 150 16.00 O 4513 8.00 N 4129 7.00 C 15425 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.33 Conformation dependent library (CDL) restraints added in 4.4 seconds 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6016 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 28 sheets defined 40.2% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.94 Creating SS restraints... Processing helix chain 'A' and resid 19 through 30 removed outlier: 3.877A pdb=" N GLU A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 102 removed outlier: 4.039A pdb=" N ARG A 84 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL A 85 " --> pdb=" O PRO A 81 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU A 86 " --> pdb=" O ASP A 82 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 120 removed outlier: 3.687A 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 167 through 177 Processing helix chain 'A' and resid 183 through 198 removed outlier: 3.996A pdb=" N SER A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 232 removed outlier: 3.718A pdb=" N ALA A 232 " --> pdb=" O ASP A 228 " (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: 3.789A pdb=" N VAL B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 121 removed outlier: 3.671A pdb=" N ILE B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 removed outlier: 3.691A pdb=" N ALA B 171 " --> pdb=" O ASN B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 201 Processing helix chain 'B' and resid 229 through 247 Processing helix chain 'C' and resid 16 through 28 removed outlier: 3.914A pdb=" N GLU C 20 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS C 28 " --> pdb=" O GLU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 76 through 99 removed outlier: 3.783A pdb=" N ALA C 80 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG C 81 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL C 83 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN C 85 " --> pdb=" O ARG C 81 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN C 92 " --> pdb=" O ARG C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 118 removed outlier: 3.986A pdb=" N TYR C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 176 removed outlier: 4.168A pdb=" N VAL C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 197 Processing helix chain 'C' and resid 221 through 235 Processing helix chain 'D' and resid 21 through 30 removed outlier: 3.670A 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 81 through 104 removed outlier: 3.968A pdb=" N ALA D 85 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR D 87 " --> pdb=" O ALA D 83 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP D 100 " --> pdb=" O THR D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 121 removed outlier: 4.020A pdb=" N LEU D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA D 120 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU D 121 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 185 Processing helix chain 'D' and resid 192 through 206 Processing helix chain 'D' and resid 230 through 240 Processing helix chain 'E' and resid 3 through 7 removed outlier: 4.245A pdb=" N ASP E 7 " --> pdb=" O ASN E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 27 removed outlier: 3.906A pdb=" N GLU E 23 " --> pdb=" O ILE E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.537A pdb=" N GLY E 32 " --> pdb=" O VAL E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 100 Processing helix chain 'E' and resid 104 through 118 removed outlier: 4.007A 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 176 Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 183 through 197 removed outlier: 3.786A pdb=" N GLU E 197 " --> pdb=" O ARG E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 233 Proline residue: E 231 - end of helix Processing helix chain 'F' and resid 21 through 30 removed outlier: 3.809A pdb=" N GLU F 25 " --> pdb=" O VAL F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 34 removed outlier: 3.679A pdb=" N SER F 34 " --> pdb=" O VAL F 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 31 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 181 through 185 removed outlier: 3.750A pdb=" N MET F 185 " --> pdb=" O MET F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 202 removed outlier: 4.076A pdb=" N LYS F 192 " --> pdb=" O ARG F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 222 No H-bonds generated for 'chain 'F' and resid 220 through 222' Processing helix chain 'F' and resid 229 through 244 Processing helix chain 'G' and resid 22 through 31 removed outlier: 3.815A pdb=" N GLU G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 35 removed outlier: 3.661A 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 Processing helix chain 'G' and resid 83 through 106 Processing helix chain 'G' and resid 110 through 125 removed outlier: 3.795A pdb=" N VAL G 124 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR G 125 " --> pdb=" O ILE G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 185 removed outlier: 3.911A pdb=" N LYS G 185 " --> pdb=" O LYS G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 207 removed outlier: 3.654A pdb=" N VAL G 195 " --> pdb=" O PHE G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 244 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 removed outlier: 3.584A pdb=" N LEU H 77 " --> pdb=" O LEU H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 107 removed outlier: 3.564A pdb=" N ASP H 103 " --> pdb=" O ASN H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 118 removed outlier: 3.952A pdb=" N ILE H 117 " --> pdb=" O GLY H 113 " (cutoff:3.500A) removed outlier: 3.500A 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: 3.719A 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 32 through 45 Processing helix chain 'I' and resid 61 through 65 removed outlier: 3.593A pdb=" N LYS I 65 " --> 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 154 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 removed outlier: 3.803A pdb=" N LEU I 184 " --> pdb=" O THR I 181 " (cutoff:3.500A) 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 279 removed outlier: 3.688A pdb=" N SER I 269 " --> pdb=" O ASN I 265 " (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: 3.546A pdb=" N GLY J 114 " --> pdb=" O VAL J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 135 removed outlier: 3.600A pdb=" N ARG J 135 " --> pdb=" O ASP J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 158 Processing helix chain 'J' and resid 186 through 198 Processing helix chain 'J' and resid 213 through 229 removed outlier: 3.537A pdb=" N ALA J 217 " --> pdb=" O ASN J 213 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TRP J 227 " --> pdb=" O TYR J 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 33 removed outlier: 3.676A pdb=" N VAL K 24 " --> pdb=" O ARG K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 114 Processing helix chain 'K' and resid 118 through 133 removed outlier: 3.567A pdb=" N ALA K 122 " --> pdb=" O ARG K 118 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR K 133 " --> pdb=" O MET K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 174 through 184 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 98 removed outlier: 4.182A pdb=" N LYS L 98 " --> pdb=" O LEU L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 153 removed outlier: 3.667A pdb=" N CYS L 150 " --> pdb=" O MET L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 175 removed outlier: 3.521A pdb=" N VAL L 175 " --> pdb=" O MET L 171 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 72 Processing helix chain 'M' and resid 76 through 93 removed outlier: 3.723A pdb=" N ARG M 93 " --> pdb=" O ALA M 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 146 Processing helix chain 'M' and resid 152 through 171 Processing helix chain 'N' and resid 3 through 8 removed outlier: 3.546A pdb=" N LEU N 7 " --> pdb=" O LEU N 3 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU N 8 " --> pdb=" O ALA N 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 3 through 8' Processing helix chain 'N' and resid 107 through 130 Processing helix chain 'N' and resid 134 through 149 removed outlier: 3.625A pdb=" N GLN N 148 " --> pdb=" O ASN N 144 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR N 149 " --> pdb=" O MET N 145 " (cutoff:3.500A) Processing helix chain 'N' and resid 190 through 201 removed outlier: 4.391A pdb=" N ALA N 194 " --> pdb=" O GLY N 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 207 through 223 Processing helix chain 'O' and resid 85 through 108 Processing helix chain 'O' and resid 112 through 127 removed outlier: 4.080A pdb=" N ARG O 127 " --> pdb=" O ILE O 123 " (cutoff:3.500A) Processing helix chain 'O' and resid 195 through 211 removed outlier: 4.259A pdb=" N PHE O 207 " --> pdb=" O VAL O 203 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE O 208 " --> pdb=" O LYS O 204 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 163 removed outlier: 3.836A pdb=" N GLY A 43 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN A 214 " --> pdb=" O GLY A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 67 removed outlier: 3.755A pdb=" N SER A 133 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 161 through 164 removed outlier: 3.610A pdb=" N ILE B 37 " --> pdb=" O LEU B 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.694A pdb=" N LEU B 134 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY B 138 " --> pdb=" O GLN B 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 158 through 161 removed outlier: 3.519A pdb=" N ASN C 159 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 43 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 62 through 64 removed outlier: 3.806A pdb=" N ALA C 131 " --> pdb=" O THR C 147 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 167 through 170 removed outlier: 3.591A pdb=" N GLY D 39 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY D 45 " --> pdb=" O THR D 42 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 74 through 75 removed outlier: 3.927A pdb=" N GLY D 144 " --> pdb=" O GLY D 75 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 158 through 161 removed outlier: 3.542A pdb=" N ILE E 212 " --> pdb=" O TYR E 224 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 63 through 65 removed outlier: 3.758A pdb=" N ILE E 72 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP E 138 " --> pdb=" O GLY E 141 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 163 through 166 removed outlier: 3.907A pdb=" N GLY F 45 " --> pdb=" O CYS F 42 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP F 216 " --> pdb=" O GLU F 226 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 67 through 71 removed outlier: 3.558A pdb=" N MET F 76 " --> pdb=" O PHE F 68 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL F 74 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY F 139 " --> pdb=" O GLY F 75 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE F 136 " --> pdb=" O ILE F 152 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR F 159 " --> pdb=" O MET F 151 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 165 through 169 removed outlier: 6.249A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 69 through 73 removed outlier: 6.610A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY G 148 " --> pdb=" O ASP G 144 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL G 151 " --> pdb=" O PHE G 163 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 48 through 50 removed outlier: 3.553A pdb=" N ARG I 48 " --> pdb=" O LYS I 100 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N PHE I 123 " --> pdb=" O VAL I 96 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N CYS I 98 " --> pdb=" O CYS I 121 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N CYS I 121 " --> pdb=" O CYS I 98 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N VAL I 132 " --> pdb=" O LEU I 126 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LYS I 70 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N CYS I 135 " --> pdb=" O LYS I 70 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE I 72 " --> pdb=" O CYS I 135 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N CYS I 137 " --> pdb=" O ILE I 72 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ALA I 74 " --> pdb=" O CYS I 137 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N CYS I 169 " --> pdb=" O ILE I 75 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE I 188 " --> pdb=" O TYR I 236 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 212 through 213 Processing sheet with id=AB8, first strand: chain 'J' and resid 1 through 4 removed outlier: 3.501A pdb=" N SER J 42 " --> pdb=" O SER J 79 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL J 77 " --> pdb=" O ILE J 44 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N TYR J 46 " --> pdb=" O ALA J 75 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N ALA J 75 " --> pdb=" O TYR J 46 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N THR J 16 " --> pdb=" O VAL J 86 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N LEU J 88 " --> pdb=" O THR J 16 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU J 18 " --> pdb=" O LEU J 88 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N LEU J 90 " --> pdb=" O LEU J 18 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL J 118 " --> pdb=" O ALA J 202 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N LEU J 204 " --> pdb=" O VAL J 118 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL J 120 " --> pdb=" O LEU J 204 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N LYS J 206 " --> pdb=" O VAL J 120 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N SER J 124 " --> pdb=" O VAL J 208 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 1 through 4 removed outlier: 3.501A pdb=" N SER J 42 " --> pdb=" O SER J 79 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL J 77 " --> pdb=" O ILE J 44 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N TYR J 46 " --> pdb=" O ALA J 75 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N ALA J 75 " --> pdb=" O TYR J 46 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N THR J 16 " --> pdb=" O VAL J 86 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N LEU J 88 " --> pdb=" O THR J 16 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU J 18 " --> pdb=" O LEU J 88 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N LEU J 90 " --> pdb=" O LEU J 18 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL J 118 " --> pdb=" O ALA J 202 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N LEU J 204 " --> pdb=" O VAL J 118 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL J 120 " --> pdb=" O LEU J 204 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N LYS J 206 " --> pdb=" O VAL J 120 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU J 205 " --> pdb=" O ARG J 140 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 167 through 170 removed outlier: 3.693A pdb=" N GLY K 54 " --> pdb=" O TYR K 51 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 78 through 81 removed outlier: 5.413A pdb=" N PHE K 79 " --> pdb=" O CYS K 86 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N CYS K 86 " --> pdb=" O PHE K 79 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 252 through 259 removed outlier: 5.584A pdb=" N UNK K 254 " --> pdb=" O LYS L 201 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LYS L 201 " --> pdb=" O UNK K 254 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR L 197 " --> pdb=" O UNK K 258 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE L 190 " --> pdb=" O VAL L 20 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL L 20 " --> pdb=" O ILE L 190 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 42 through 44 removed outlier: 3.500A pdb=" N ILE L 109 " --> pdb=" O CYS L 122 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 129 through 132 Processing sheet with id=AC6, first strand: chain 'M' and resid 35 through 37 removed outlier: 3.602A pdb=" N LEU M 102 " --> pdb=" O MET M 118 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 184 through 187 removed outlier: 3.771A pdb=" N ASN N 234 " --> pdb=" O ALA N 75 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY N 242 " --> pdb=" O ARG N 239 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 93 through 94 removed outlier: 4.095A pdb=" N MET N 159 " --> pdb=" O THR N 103 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 163 through 164 removed outlier: 3.924A pdb=" N VAL O 51 " --> pdb=" O CYS O 224 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 70 through 75 removed outlier: 3.677A pdb=" N LYS O 70 " --> pdb=" O CYS O 82 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR O 78 " --> pdb=" O LEU O 74 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL O 149 " --> pdb=" O ASP O 161 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN O 159 " --> pdb=" O SER O 151 " (cutoff:3.500A) 1264 hydrogen bonds defined for protein. 3621 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: 7.92 Time building geometry restraints manager: 10.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7900 1.34 - 1.46: 3319 1.46 - 1.57: 13200 1.57 - 1.69: 0 1.69 - 1.81: 235 Bond restraints: 24654 Sorted by residual: bond pdb=" N ASP L 134 " pdb=" CA ASP L 134 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.27e-02 6.20e+03 6.48e+00 bond pdb=" C ACE J 0 " pdb=" O ACE J 0 " ideal model delta sigma weight residual 1.199 1.229 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" C ACE G 0 " pdb=" O ACE G 0 " ideal model delta sigma weight residual 1.199 1.229 -0.030 2.00e-02 2.50e+03 2.29e+00 bond pdb=" C ACE M 0 " pdb=" O ACE M 0 " ideal model delta sigma weight residual 1.199 1.229 -0.030 2.00e-02 2.50e+03 2.24e+00 bond pdb=" C ACE E 0 " pdb=" O ACE E 0 " ideal model delta sigma weight residual 1.199 1.228 -0.029 2.00e-02 2.50e+03 2.07e+00 ... (remaining 24649 not shown) Histogram of bond angle deviations from ideal: 98.23 - 105.39: 433 105.39 - 112.56: 12954 112.56 - 119.72: 7878 119.72 - 126.88: 11952 126.88 - 134.04: 234 Bond angle restraints: 33451 Sorted by residual: angle pdb=" N ILE C 181 " pdb=" CA ILE C 181 " pdb=" C ILE C 181 " ideal model delta sigma weight residual 113.20 107.59 5.61 9.60e-01 1.09e+00 3.41e+01 angle pdb=" N ILE L 127 " pdb=" CA ILE L 127 " pdb=" C ILE L 127 " ideal model delta sigma weight residual 111.81 109.06 2.75 8.60e-01 1.35e+00 1.02e+01 angle pdb=" C ASP H 29 " pdb=" N LEU H 30 " pdb=" CA LEU H 30 " ideal model delta sigma weight residual 121.54 126.73 -5.19 1.91e+00 2.74e-01 7.40e+00 angle pdb=" C GLN I 208 " pdb=" N PRO I 209 " pdb=" CA PRO I 209 " ideal model delta sigma weight residual 121.91 118.56 3.35 1.35e+00 5.49e-01 6.17e+00 angle pdb=" N LYS M 34 " pdb=" CA LYS M 34 " pdb=" C LYS M 34 " ideal model delta sigma weight residual 114.56 111.46 3.10 1.27e+00 6.20e-01 5.95e+00 ... (remaining 33446 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 13462 17.74 - 35.47: 1061 35.47 - 53.21: 173 53.21 - 70.95: 45 70.95 - 88.68: 15 Dihedral angle restraints: 14756 sinusoidal: 5409 harmonic: 9347 Sorted by residual: dihedral pdb=" CA PHE G 9 " pdb=" C PHE G 9 " pdb=" N ASP G 10 " pdb=" CA ASP G 10 " ideal model delta harmonic sigma weight residual 180.00 160.30 19.70 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA GLY D 19 " pdb=" C GLY D 19 " pdb=" N ARG D 20 " pdb=" CA ARG D 20 " ideal model delta harmonic sigma weight residual 180.00 162.31 17.69 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA LEU M 102 " pdb=" C LEU M 102 " pdb=" N LEU M 103 " pdb=" CA LEU M 103 " ideal model delta harmonic sigma weight residual 180.00 163.12 16.88 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 14753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2513 0.032 - 0.064: 953 0.064 - 0.096: 241 0.096 - 0.129: 185 0.129 - 0.161: 12 Chirality restraints: 3904 Sorted by residual: chirality pdb=" CG LEU C 96 " pdb=" CB LEU C 96 " pdb=" CD1 LEU C 96 " pdb=" CD2 LEU C 96 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.45e-01 chirality pdb=" CA ILE M 5 " pdb=" N ILE M 5 " pdb=" C ILE M 5 " pdb=" CB ILE M 5 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA PRO L 160 " pdb=" N PRO L 160 " pdb=" C PRO L 160 " pdb=" CB PRO L 160 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.57e-01 ... (remaining 3901 not shown) Planarity restraints: 4270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 216 " -0.017 2.00e-02 2.50e+03 1.70e-02 7.25e+00 pdb=" CG TRP F 216 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP F 216 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP F 216 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 216 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP F 216 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 216 " -0.001 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=" C LYS J 232 " 0.041 5.00e-02 4.00e+02 6.26e-02 6.28e+00 pdb=" N PRO J 233 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO J 233 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO J 233 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN N 97 " 0.037 5.00e-02 4.00e+02 5.65e-02 5.11e+00 pdb=" N PRO N 98 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO N 98 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO N 98 " 0.031 5.00e-02 4.00e+02 ... (remaining 4267 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2030 2.74 - 3.28: 22083 3.28 - 3.82: 36943 3.82 - 4.36: 41731 4.36 - 4.90: 79035 Nonbonded interactions: 181822 Sorted by model distance: nonbonded pdb=" OH TYR G 23 " pdb=" OD1 ASP J 131 " model vdw 2.202 3.040 nonbonded pdb=" O LYS I 275 " pdb=" OG1 THR I 278 " model vdw 2.210 3.040 nonbonded pdb=" OG SER G 17 " pdb=" OD2 ASP J 131 " model vdw 2.235 3.040 nonbonded pdb=" OD1 ASP D 157 " pdb=" OG SER D 159 " model vdw 2.244 3.040 nonbonded pdb=" OG SER A 35 " pdb=" OG SER A 77 " model vdw 2.252 3.040 ... (remaining 181817 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: 1.900 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: 0.960 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 64.460 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.090 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:10.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 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 : 0.003 0.032 24654 Z= 0.178 Angle : 0.482 6.912 33451 Z= 0.259 Chirality : 0.041 0.161 3904 Planarity : 0.004 0.063 4270 Dihedral : 13.366 88.685 8740 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.15), residues: 3147 helix: 2.82 (0.15), residues: 1137 sheet: 0.07 (0.19), residues: 717 loop : -1.34 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP F 216 HIS 0.004 0.001 HIS M 132 PHE 0.016 0.001 PHE L 69 TYR 0.024 0.001 TYR B 121 ARG 0.007 0.000 ARG I 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 2.747 Fit side-chains REVERT: B 177 GLN cc_start: 0.8536 (tt0) cc_final: 0.8160 (tp-100) REVERT: C 175 ASN cc_start: 0.8557 (m110) cc_final: 0.8175 (m110) REVERT: F 114 ASP cc_start: 0.7596 (m-30) cc_final: 0.7280 (m-30) REVERT: L 158 MET cc_start: 0.8053 (mtp) cc_final: 0.7827 (mtp) REVERT: L 192 LYS cc_start: 0.8863 (tmtt) cc_final: 0.8452 (tptm) REVERT: M 28 MET cc_start: 0.8574 (pmm) cc_final: 0.8319 (pmt) REVERT: N 217 ARG cc_start: 0.7509 (mmp80) cc_final: 0.7255 (mmp80) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 1.4389 time to fit residues: 535.4008 Evaluate side-chains 253 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 2.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 266 optimal weight: 20.0000 chunk 239 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 81 optimal weight: 9.9990 chunk 161 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 247 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 chunk 184 optimal weight: 10.0000 chunk 286 optimal weight: 2.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 GLN B 220 ASN ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 GLN F 222 ASN H 90 GLN H 99 ASN J 229 GLN L 157 ASN N 237 HIS O 136 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 24654 Z= 0.311 Angle : 0.568 8.549 33451 Z= 0.300 Chirality : 0.044 0.167 3904 Planarity : 0.005 0.054 4270 Dihedral : 4.196 32.849 3480 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.05 % Allowed : 8.38 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.15), residues: 3147 helix: 2.75 (0.15), residues: 1146 sheet: 0.18 (0.19), residues: 704 loop : -1.36 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 216 HIS 0.006 0.001 HIS M 132 PHE 0.020 0.001 PHE L 69 TYR 0.030 0.001 TYR B 121 ARG 0.005 0.000 ARG H 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 271 time to evaluate : 2.948 Fit side-chains REVERT: B 177 GLN cc_start: 0.8557 (tt0) cc_final: 0.8159 (tp-100) REVERT: C 175 ASN cc_start: 0.8579 (m110) cc_final: 0.8176 (m110) REVERT: D 90 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.8002 (OUTLIER) REVERT: D 118 ASN cc_start: 0.8608 (OUTLIER) cc_final: 0.8142 (t160) REVERT: F 114 ASP cc_start: 0.7612 (m-30) cc_final: 0.7292 (m-30) REVERT: G 120 ASP cc_start: 0.8471 (m-30) cc_final: 0.8230 (m-30) REVERT: H 90 GLN cc_start: 0.8673 (mt0) cc_final: 0.8437 (mt0) REVERT: I 265 ASN cc_start: 0.7448 (t0) cc_final: 0.6965 (t0) REVERT: K 96 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.7364 (m-30) REVERT: L 192 LYS cc_start: 0.8901 (tmtt) cc_final: 0.8430 (tptm) REVERT: M 28 MET cc_start: 0.8507 (pmm) cc_final: 0.8278 (pmt) REVERT: M 108 ASP cc_start: 0.8400 (t0) cc_final: 0.8073 (t0) outliers start: 26 outliers final: 10 residues processed: 282 average time/residue: 1.4017 time to fit residues: 451.4902 Evaluate side-chains 257 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 245 time to evaluate : 2.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 161 ASP Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain O residue 101 LYS Chi-restraints excluded: chain O residue 113 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 159 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 238 optimal weight: 6.9990 chunk 195 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 287 optimal weight: 5.9990 chunk 310 optimal weight: 10.0000 chunk 256 optimal weight: 9.9990 chunk 285 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 230 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 145 GLN L 157 ASN M 186 ASN N 144 ASN O 136 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 24654 Z= 0.421 Angle : 0.601 10.107 33451 Z= 0.317 Chirality : 0.045 0.166 3904 Planarity : 0.005 0.059 4270 Dihedral : 4.438 39.439 3480 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.07 % Allowed : 10.45 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.15), residues: 3147 helix: 2.58 (0.15), residues: 1144 sheet: 0.26 (0.19), residues: 701 loop : -1.47 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 216 HIS 0.006 0.001 HIS M 132 PHE 0.024 0.002 PHE L 69 TYR 0.041 0.002 TYR B 121 ARG 0.006 0.000 ARG I 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 255 time to evaluate : 2.713 Fit side-chains revert: symmetry clash REVERT: B 177 GLN cc_start: 0.8574 (tt0) cc_final: 0.8188 (tp-100) REVERT: C 175 ASN cc_start: 0.8565 (m110) cc_final: 0.8109 (m110) REVERT: D 90 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.8013 (t0) REVERT: D 118 ASN cc_start: 0.8646 (OUTLIER) cc_final: 0.8183 (t160) REVERT: E 27 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7321 (tm-30) REVERT: H 62 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7982 (tpt) REVERT: I 265 ASN cc_start: 0.7455 (t0) cc_final: 0.6922 (t0) REVERT: J 50 ASP cc_start: 0.8478 (p0) cc_final: 0.8219 (p0) REVERT: J 83 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.7665 (mtm180) REVERT: K 96 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7460 (m-30) REVERT: L 12 MET cc_start: 0.8433 (ttt) cc_final: 0.7624 (ttt) REVERT: L 192 LYS cc_start: 0.8916 (tmtt) cc_final: 0.8405 (tptm) REVERT: M 28 MET cc_start: 0.8417 (pmm) cc_final: 0.8187 (pmt) outliers start: 51 outliers final: 15 residues processed: 288 average time/residue: 1.3727 time to fit residues: 452.7165 Evaluate side-chains 261 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 240 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 83 ARG Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain N residue 62 THR Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain O residue 101 LYS Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain O residue 164 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 284 optimal weight: 2.9990 chunk 216 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 chunk 193 optimal weight: 0.0270 chunk 288 optimal weight: 6.9990 chunk 305 optimal weight: 7.9990 chunk 150 optimal weight: 0.9980 chunk 273 optimal weight: 0.0030 chunk 82 optimal weight: 1.9990 overall best weight: 0.5650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN F 98 ASN J 229 GLN M 99 HIS M 186 ASN N 144 ASN O 136 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 24654 Z= 0.127 Angle : 0.477 8.039 33451 Z= 0.254 Chirality : 0.041 0.162 3904 Planarity : 0.004 0.058 4270 Dihedral : 3.979 33.942 3480 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.42 % Allowed : 12.03 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.15), residues: 3147 helix: 2.94 (0.15), residues: 1134 sheet: 0.42 (0.19), residues: 694 loop : -1.25 (0.16), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 216 HIS 0.004 0.000 HIS I 125 PHE 0.015 0.001 PHE K 207 TYR 0.012 0.001 TYR K 51 ARG 0.007 0.000 ARG I 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 275 time to evaluate : 2.745 Fit side-chains revert: symmetry clash REVERT: B 177 GLN cc_start: 0.8547 (tt0) cc_final: 0.8148 (tp-100) REVERT: C 175 ASN cc_start: 0.8495 (m110) cc_final: 0.8102 (m110) REVERT: F 114 ASP cc_start: 0.7587 (m-30) cc_final: 0.7257 (m-30) REVERT: H 62 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7947 (tpt) REVERT: I 265 ASN cc_start: 0.7385 (t0) cc_final: 0.6803 (t0) REVERT: J 50 ASP cc_start: 0.8424 (p0) cc_final: 0.8178 (p0) REVERT: L 192 LYS cc_start: 0.8884 (tmtt) cc_final: 0.8379 (tptm) REVERT: O 164 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6832 (tppt) outliers start: 35 outliers final: 7 residues processed: 297 average time/residue: 1.1290 time to fit residues: 384.4428 Evaluate side-chains 255 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 246 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain L residue 135 ASP Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain M residue 132 HIS Chi-restraints excluded: chain O residue 164 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 254 optimal weight: 0.9980 chunk 173 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 227 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 260 optimal weight: 7.9990 chunk 211 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 155 optimal weight: 0.8980 chunk 274 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 229 GLN L 145 GLN M 8 GLN M 186 ASN O 136 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24654 Z= 0.209 Angle : 0.506 8.013 33451 Z= 0.268 Chirality : 0.042 0.161 3904 Planarity : 0.004 0.056 4270 Dihedral : 3.989 36.501 3480 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.66 % Allowed : 13.73 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.15), residues: 3147 helix: 3.00 (0.15), residues: 1134 sheet: 0.49 (0.20), residues: 693 loop : -1.24 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 216 HIS 0.004 0.001 HIS I 125 PHE 0.017 0.001 PHE L 69 TYR 0.021 0.001 TYR O 158 ARG 0.008 0.000 ARG N 217 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 247 time to evaluate : 2.661 Fit side-chains revert: symmetry clash REVERT: B 177 GLN cc_start: 0.8569 (tt0) cc_final: 0.8157 (tp-100) REVERT: C 175 ASN cc_start: 0.8531 (m110) cc_final: 0.8112 (m110) REVERT: E 27 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7351 (tm-30) REVERT: F 114 ASP cc_start: 0.7638 (m-30) cc_final: 0.7311 (m-30) REVERT: G 19 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8428 (pm20) REVERT: G 120 ASP cc_start: 0.8474 (m-30) cc_final: 0.8230 (m-30) REVERT: H 62 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7969 (tpt) REVERT: I 265 ASN cc_start: 0.7322 (t0) cc_final: 0.6716 (t0) REVERT: J 50 ASP cc_start: 0.8411 (p0) cc_final: 0.8162 (p0) REVERT: L 192 LYS cc_start: 0.8895 (tmtt) cc_final: 0.8378 (tptm) REVERT: M 28 MET cc_start: 0.8376 (pmm) cc_final: 0.7919 (pmm) REVERT: M 99 HIS cc_start: 0.8485 (OUTLIER) cc_final: 0.8252 (m-70) REVERT: O 164 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6620 (tppt) outliers start: 41 outliers final: 15 residues processed: 272 average time/residue: 1.2354 time to fit residues: 384.2795 Evaluate side-chains 260 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 240 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 135 ASP Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain M residue 11 ASP Chi-restraints excluded: chain M residue 99 HIS Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain O residue 164 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 102 optimal weight: 9.9990 chunk 275 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 305 optimal weight: 9.9990 chunk 253 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 160 optimal weight: 0.0060 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 229 GLN M 186 ASN O 136 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24654 Z= 0.181 Angle : 0.495 9.421 33451 Z= 0.262 Chirality : 0.041 0.157 3904 Planarity : 0.004 0.055 4270 Dihedral : 3.960 37.765 3480 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.86 % Allowed : 13.69 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.15), residues: 3147 helix: 3.01 (0.15), residues: 1136 sheet: 0.53 (0.20), residues: 693 loop : -1.25 (0.16), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 216 HIS 0.004 0.001 HIS I 125 PHE 0.015 0.001 PHE L 69 TYR 0.015 0.001 TYR K 51 ARG 0.009 0.000 ARG N 217 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 252 time to evaluate : 3.157 Fit side-chains revert: symmetry clash REVERT: B 177 GLN cc_start: 0.8577 (tt0) cc_final: 0.8161 (tp-100) REVERT: C 175 ASN cc_start: 0.8530 (m110) cc_final: 0.8117 (m110) REVERT: D 1 MET cc_start: 0.8718 (mmt) cc_final: 0.8161 (mmt) REVERT: D 78 MET cc_start: 0.8140 (mmm) cc_final: 0.7873 (tpp) REVERT: E 27 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7354 (tm-30) REVERT: F 114 ASP cc_start: 0.7631 (m-30) cc_final: 0.7292 (m-30) REVERT: G 120 ASP cc_start: 0.8461 (m-30) cc_final: 0.8216 (m-30) REVERT: H 62 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7962 (tpt) REVERT: I 265 ASN cc_start: 0.7332 (t0) cc_final: 0.6740 (t0) REVERT: J 50 ASP cc_start: 0.8372 (p0) cc_final: 0.8112 (p0) REVERT: L 192 LYS cc_start: 0.8886 (tmtt) cc_final: 0.8357 (tptm) REVERT: M 11 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8108 (t0) REVERT: M 28 MET cc_start: 0.8392 (pmm) cc_final: 0.7938 (pmm) REVERT: M 99 HIS cc_start: 0.8464 (OUTLIER) cc_final: 0.8218 (m-70) REVERT: O 164 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6616 (tppt) outliers start: 46 outliers final: 23 residues processed: 283 average time/residue: 1.3430 time to fit residues: 437.0429 Evaluate side-chains 267 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 239 time to evaluate : 2.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 135 ASP Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 161 ASP Chi-restraints excluded: chain M residue 11 ASP Chi-restraints excluded: chain M residue 99 HIS Chi-restraints excluded: chain M residue 132 HIS Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain N residue 198 MET Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain O residue 164 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 294 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 174 optimal weight: 3.9990 chunk 223 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 257 optimal weight: 8.9990 chunk 170 optimal weight: 5.9990 chunk 304 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 chunk 185 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 186 ASN O 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 24654 Z= 0.417 Angle : 0.592 8.928 33451 Z= 0.312 Chirality : 0.045 0.168 3904 Planarity : 0.005 0.060 4270 Dihedral : 4.324 42.424 3480 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.11 % Allowed : 14.30 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.15), residues: 3147 helix: 2.75 (0.15), residues: 1142 sheet: 0.41 (0.19), residues: 707 loop : -1.42 (0.16), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 216 HIS 0.005 0.001 HIS I 125 PHE 0.025 0.002 PHE L 69 TYR 0.029 0.002 TYR B 121 ARG 0.011 0.000 ARG I 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 239 time to evaluate : 2.961 Fit side-chains REVERT: B 177 GLN cc_start: 0.8599 (tt0) cc_final: 0.8191 (tp-100) REVERT: C 175 ASN cc_start: 0.8560 (m110) cc_final: 0.8080 (m110) REVERT: D 1 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8792 (mmt) REVERT: D 78 MET cc_start: 0.8341 (mmm) cc_final: 0.8092 (tpp) REVERT: D 90 ASP cc_start: 0.8414 (m-30) cc_final: 0.8015 (t0) REVERT: E 27 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7346 (tm-30) REVERT: E 203 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7448 (mm-40) REVERT: G 120 ASP cc_start: 0.8503 (m-30) cc_final: 0.8267 (m-30) REVERT: H 62 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.7975 (tpt) REVERT: I 146 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.6165 (mm-40) REVERT: I 265 ASN cc_start: 0.7397 (t0) cc_final: 0.6815 (t0) REVERT: J 50 ASP cc_start: 0.8400 (p0) cc_final: 0.8117 (p0) REVERT: K 96 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7449 (m-30) REVERT: L 192 LYS cc_start: 0.8933 (tmtt) cc_final: 0.8406 (tptm) REVERT: M 99 HIS cc_start: 0.8591 (OUTLIER) cc_final: 0.8268 (m-70) REVERT: O 164 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.6690 (tppt) outliers start: 52 outliers final: 27 residues processed: 275 average time/residue: 1.4296 time to fit residues: 448.5873 Evaluate side-chains 266 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 231 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 47 CYS Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain I residue 146 GLN Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 135 ASP Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 150 CYS Chi-restraints excluded: chain L residue 161 ASP Chi-restraints excluded: chain M residue 99 HIS Chi-restraints excluded: chain M residue 132 HIS Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain O residue 164 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 188 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 181 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 193 optimal weight: 0.0030 chunk 207 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 239 optimal weight: 1.9990 chunk 277 optimal weight: 30.0000 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 186 ASN O 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24654 Z= 0.225 Angle : 0.530 8.172 33451 Z= 0.281 Chirality : 0.042 0.191 3904 Planarity : 0.005 0.059 4270 Dihedral : 4.200 41.601 3480 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.86 % Allowed : 14.86 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.15), residues: 3147 helix: 2.83 (0.15), residues: 1143 sheet: 0.45 (0.19), residues: 701 loop : -1.40 (0.16), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 216 HIS 0.005 0.001 HIS I 125 PHE 0.017 0.001 PHE L 69 TYR 0.016 0.001 TYR K 51 ARG 0.011 0.000 ARG I 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 242 time to evaluate : 2.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 177 GLN cc_start: 0.8591 (tt0) cc_final: 0.8189 (tp-100) REVERT: C 175 ASN cc_start: 0.8545 (m110) cc_final: 0.8065 (m110) REVERT: D 78 MET cc_start: 0.8203 (mmm) cc_final: 0.7980 (tpp) REVERT: D 90 ASP cc_start: 0.8368 (m-30) cc_final: 0.8007 (OUTLIER) REVERT: E 27 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7332 (tm-30) REVERT: E 203 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7449 (mm-40) REVERT: H 62 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7940 (tpt) REVERT: I 146 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.5963 (mm-40) REVERT: I 265 ASN cc_start: 0.7353 (t0) cc_final: 0.6758 (t0) REVERT: J 50 ASP cc_start: 0.8386 (p0) cc_final: 0.8093 (p0) REVERT: L 192 LYS cc_start: 0.8909 (tmtt) cc_final: 0.8375 (tptm) REVERT: M 99 HIS cc_start: 0.8575 (OUTLIER) cc_final: 0.8283 (m-70) REVERT: M 108 ASP cc_start: 0.8349 (t0) cc_final: 0.8081 (t0) REVERT: O 164 LYS cc_start: 0.7265 (OUTLIER) cc_final: 0.6678 (tppt) outliers start: 46 outliers final: 28 residues processed: 271 average time/residue: 1.3646 time to fit residues: 425.1188 Evaluate side-chains 267 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 234 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 47 CYS Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain I residue 146 GLN Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 135 ASP Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 150 CYS Chi-restraints excluded: chain L residue 161 ASP Chi-restraints excluded: chain M residue 99 HIS Chi-restraints excluded: chain M residue 132 HIS Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain N residue 198 MET Chi-restraints excluded: chain O residue 77 LYS Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain O residue 164 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 291 optimal weight: 9.9990 chunk 266 optimal weight: 9.9990 chunk 283 optimal weight: 0.6980 chunk 170 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 222 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 256 optimal weight: 5.9990 chunk 268 optimal weight: 9.9990 chunk 282 optimal weight: 7.9990 chunk 186 optimal weight: 9.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 186 ASN O 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 24654 Z= 0.336 Angle : 0.574 9.517 33451 Z= 0.302 Chirality : 0.044 0.167 3904 Planarity : 0.005 0.059 4270 Dihedral : 4.314 42.976 3480 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.78 % Allowed : 15.23 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.15), residues: 3147 helix: 2.74 (0.15), residues: 1141 sheet: 0.39 (0.19), residues: 708 loop : -1.45 (0.16), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 216 HIS 0.005 0.001 HIS I 125 PHE 0.021 0.001 PHE L 69 TYR 0.022 0.001 TYR B 121 ARG 0.014 0.000 ARG N 217 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 237 time to evaluate : 2.701 Fit side-chains revert: symmetry clash REVERT: B 177 GLN cc_start: 0.8599 (tt0) cc_final: 0.8193 (tp-100) REVERT: C 175 ASN cc_start: 0.8545 (m110) cc_final: 0.8059 (m110) REVERT: D 90 ASP cc_start: 0.8406 (m-30) cc_final: 0.8013 (t0) REVERT: E 27 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: E 203 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7459 (mm-40) REVERT: H 62 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7956 (tpt) REVERT: I 146 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.6000 (mm-40) REVERT: I 265 ASN cc_start: 0.7391 (t0) cc_final: 0.6805 (t0) REVERT: J 50 ASP cc_start: 0.8405 (p0) cc_final: 0.8128 (p0) REVERT: L 192 LYS cc_start: 0.8929 (tmtt) cc_final: 0.8395 (tptm) REVERT: M 99 HIS cc_start: 0.8610 (OUTLIER) cc_final: 0.8345 (m-70) REVERT: M 108 ASP cc_start: 0.8420 (t0) cc_final: 0.8132 (t0) REVERT: O 104 LYS cc_start: 0.8614 (ttpt) cc_final: 0.8085 (tptt) REVERT: O 164 LYS cc_start: 0.7287 (OUTLIER) cc_final: 0.6732 (tppt) outliers start: 44 outliers final: 31 residues processed: 267 average time/residue: 1.3628 time to fit residues: 418.5613 Evaluate side-chains 269 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 232 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 47 CYS Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain I residue 146 GLN Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 135 ASP Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 150 CYS Chi-restraints excluded: chain L residue 161 ASP Chi-restraints excluded: chain M residue 99 HIS Chi-restraints excluded: chain M residue 132 HIS Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 198 MET Chi-restraints excluded: chain O residue 77 LYS Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain O residue 164 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 300 optimal weight: 40.0000 chunk 183 optimal weight: 7.9990 chunk 142 optimal weight: 1.9990 chunk 208 optimal weight: 3.9990 chunk 314 optimal weight: 30.0000 chunk 289 optimal weight: 9.9990 chunk 250 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 193 optimal weight: 9.9990 chunk 153 optimal weight: 4.9990 chunk 199 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 229 GLN M 186 ASN O 136 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24654 Z= 0.241 Angle : 0.541 9.247 33451 Z= 0.287 Chirality : 0.042 0.182 3904 Planarity : 0.005 0.061 4270 Dihedral : 4.247 43.041 3480 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.42 % Allowed : 15.76 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.15), residues: 3147 helix: 2.81 (0.15), residues: 1142 sheet: 0.41 (0.19), residues: 709 loop : -1.40 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 216 HIS 0.005 0.001 HIS I 125 PHE 0.017 0.001 PHE L 69 TYR 0.016 0.001 TYR K 51 ARG 0.017 0.000 ARG N 217 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 239 time to evaluate : 2.881 Fit side-chains revert: symmetry clash REVERT: B 177 GLN cc_start: 0.8595 (tt0) cc_final: 0.8192 (tp-100) REVERT: C 175 ASN cc_start: 0.8546 (m110) cc_final: 0.8049 (m110) REVERT: E 27 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7325 (tm-30) REVERT: E 203 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7459 (mm-40) REVERT: H 62 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7944 (tpt) REVERT: I 146 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.5883 (mm-40) REVERT: I 265 ASN cc_start: 0.7348 (t0) cc_final: 0.6748 (t0) REVERT: J 50 ASP cc_start: 0.8384 (p0) cc_final: 0.8099 (p0) REVERT: L 192 LYS cc_start: 0.8920 (tmtt) cc_final: 0.8385 (tptm) REVERT: M 99 HIS cc_start: 0.8606 (OUTLIER) cc_final: 0.8336 (m-70) REVERT: O 104 LYS cc_start: 0.8590 (ttpt) cc_final: 0.8061 (tptt) REVERT: O 164 LYS cc_start: 0.7237 (OUTLIER) cc_final: 0.6649 (tppt) outliers start: 35 outliers final: 29 residues processed: 265 average time/residue: 1.3410 time to fit residues: 408.6956 Evaluate side-chains 268 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 233 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 47 CYS Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain I residue 146 GLN Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 135 ASP Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 150 CYS Chi-restraints excluded: chain L residue 161 ASP Chi-restraints excluded: chain M residue 99 HIS Chi-restraints excluded: chain M residue 132 HIS Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain N residue 198 MET Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain O residue 164 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 267 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 231 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 251 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 257 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 220 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.094825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.065886 restraints weight = 47325.261| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.87 r_work: 0.2746 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24654 Z= 0.222 Angle : 0.534 11.909 33451 Z= 0.281 Chirality : 0.042 0.167 3904 Planarity : 0.005 0.060 4270 Dihedral : 4.205 43.694 3480 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.42 % Allowed : 15.96 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.15), residues: 3147 helix: 2.82 (0.15), residues: 1145 sheet: 0.46 (0.19), residues: 700 loop : -1.36 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 216 HIS 0.005 0.001 HIS I 125 PHE 0.017 0.001 PHE L 69 TYR 0.015 0.001 TYR K 51 ARG 0.018 0.000 ARG N 217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7455.94 seconds wall clock time: 133 minutes 59.30 seconds (8039.30 seconds total)