Starting phenix.real_space_refine on Mon May 13 07:20:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qz9_18773/05_2024/8qz9_18773_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qz9_18773/05_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_18773/05_2024/8qz9_18773.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qz9_18773/05_2024/8qz9_18773.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qz9_18773/05_2024/8qz9_18773_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qz9_18773/05_2024/8qz9_18773_updated.pdb" } 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 24217 Number of models: 1 Model: "" Number of chains: 15 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: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1646 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 11, 'TRANS': 219} Chain breaks: 3 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'TYR:plan': 1, 'UNK:plan-1': 16, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 57 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: 12.54, per 1000 atoms: 0.52 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: 9.05 Conformation dependent library (CDL) restraints added in 4.5 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... running ksdssp... Secondary structure from input PDB file: 90 helices and 25 sheets defined 35.3% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.50 Creating SS restraints... Processing helix chain 'A' and resid 20 through 31 removed outlier: 3.520A pdb=" N GLY A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 101 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 107 through 122 removed outlier: 3.687A pdb=" N GLU A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TYR A 121 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N THR A 122 " --> pdb=" O MET A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 176 Processing helix chain 'A' and resid 184 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 223 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 19 through 30 removed outlier: 4.031A pdb=" N ILE B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY B 29 " --> pdb=" O MET B 25 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N HIS B 30 " --> pdb=" O GLU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 101 removed outlier: 3.789A pdb=" N VAL B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 122 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) removed outlier: 4.388A pdb=" N THR B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 178 Processing helix chain 'B' and resid 186 through 200 Processing helix chain 'B' and resid 230 through 246 Processing helix chain 'C' and resid 17 through 28 removed outlier: 3.666A pdb=" N LYS C 28 " --> pdb=" O GLU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 98 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 104 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 165 through 175 Processing helix chain 'C' and resid 184 through 196 Processing helix chain 'C' and resid 222 through 234 Processing helix chain 'D' and resid 22 through 33 removed outlier: 3.796A pdb=" N ILE D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LYS D 32 " --> pdb=" O ILE D 28 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LEU D 33 " --> pdb=" O GLU D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 63 No H-bonds generated for 'chain 'D' and resid 61 through 63' Processing helix chain 'D' and resid 82 through 103 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 109 through 120 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) Processing helix chain 'D' and resid 174 through 184 Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 231 through 239 Processing helix chain 'E' and resid 4 through 6 No H-bonds generated for 'chain 'E' and resid 4 through 6' Processing helix chain 'E' and resid 20 through 31 removed outlier: 3.700A pdb=" N ALA E 28 " --> pdb=" O TYR E 24 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL E 29 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LYS E 30 " --> pdb=" O MET E 26 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLN E 31 " --> pdb=" O GLU E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 99 Processing helix chain 'E' and resid 105 through 120 removed outlier: 4.007A pdb=" N ILE E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) Proline residue: E 119 - end of helix Processing helix chain 'E' and resid 166 through 178 removed outlier: 5.303A pdb=" N SER E 177 " --> pdb=" O GLU E 173 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLU E 178 " --> pdb=" O ARG E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 198 removed outlier: 3.786A pdb=" N GLU E 197 " --> pdb=" O ARG E 193 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR E 198 " --> pdb=" O ALA E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 232 Proline residue: E 231 - end of helix Processing helix chain 'F' and resid 22 through 33 removed outlier: 3.764A pdb=" N VAL F 31 " --> pdb=" O ALA F 27 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLU F 32 " --> pdb=" O MET F 28 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASN F 33 " --> pdb=" O LYS F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 103 Processing helix chain 'F' and resid 109 through 124 removed outlier: 4.151A pdb=" N TYR F 123 " --> pdb=" O TYR F 119 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR F 124 " --> pdb=" O VAL F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 177 Processing helix chain 'F' and resid 182 through 184 No H-bonds generated for 'chain 'F' and resid 182 through 184' Processing helix chain 'F' and resid 187 through 201 removed outlier: 4.076A pdb=" N LYS F 192 " --> pdb=" O ARG F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 221 No H-bonds generated for 'chain 'F' and resid 219 through 221' Processing helix chain 'F' and resid 230 through 243 Processing helix chain 'G' and resid 23 through 34 removed outlier: 3.775A pdb=" N ILE G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASN G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLN G 34 " --> pdb=" O LYS G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 65 No H-bonds generated for 'chain 'G' and resid 63 through 65' Processing helix chain 'G' and resid 84 through 105 Processing helix chain 'G' and resid 111 through 126 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) removed outlier: 4.093A pdb=" N THR G 126 " --> pdb=" O SER G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 184 Processing helix chain 'G' and resid 191 through 206 removed outlier: 3.654A pdb=" N VAL G 195 " --> pdb=" O PHE G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 243 Processing helix chain 'H' and resid 49 through 53 Processing helix chain 'H' and resid 55 through 70 Processing helix chain 'H' and resid 73 through 88 removed outlier: 3.584A pdb=" N LEU H 77 " --> pdb=" O LEU H 73 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN H 88 " --> pdb=" O LYS H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 106 Processing helix chain 'H' and resid 114 through 117 No H-bonds generated for 'chain 'H' and resid 114 through 117' Processing helix chain 'H' and resid 121 through 123 No H-bonds generated for 'chain 'H' and resid 121 through 123' Processing helix chain 'H' and resid 130 through 138 Processing helix chain 'I' and resid 32 through 45 Processing helix chain 'I' and resid 77 through 86 Processing helix chain 'I' and resid 146 through 153 Processing helix chain 'I' and resid 172 through 174 No H-bonds generated for 'chain 'I' and resid 172 through 174' Processing helix chain 'I' and resid 181 through 183 No H-bonds generated for 'chain 'I' and resid 181 through 183' Processing helix chain 'I' and resid 214 through 225 Processing helix chain 'I' and resid 244 through 255 removed outlier: 4.024A pdb=" N PHE I 250 " --> pdb=" O THR I 246 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS I 251 " --> pdb=" O VAL I 247 " (cutoff:3.500A) Proline residue: I 252 - end of helix removed outlier: 4.338A pdb=" N SER I 255 " --> pdb=" O LYS I 251 " (cutoff:3.500A) Processing helix chain 'I' and resid 266 through 278 Processing helix chain 'J' and resid 24 through 39 removed outlier: 4.056A pdb=" N VAL J 27 " --> pdb=" O VAL J 24 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N GLY J 28 " --> pdb=" O GLY J 25 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU J 39 " --> pdb=" O ILE J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 113 Processing helix chain 'J' and resid 131 through 134 No H-bonds generated for 'chain 'J' and resid 131 through 134' Processing helix chain 'J' and resid 152 through 157 Processing helix chain 'J' and resid 187 through 197 Processing helix chain 'J' and resid 214 through 228 removed outlier: 3.996A pdb=" N TRP J 227 " --> pdb=" O TYR J 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 32 removed outlier: 3.676A pdb=" N VAL K 24 " --> pdb=" O ARG K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 113 Processing helix chain 'K' and resid 119 through 132 Processing helix chain 'K' and resid 175 through 183 Processing helix chain 'K' and resid 191 through 205 removed outlier: 3.873A pdb=" N GLY K 205 " --> pdb=" O ALA K 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 223 through 225 No H-bonds generated for 'chain 'K' and resid 223 through 225' Processing helix chain 'L' and resid 57 through 78 Processing helix chain 'L' and resid 84 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 147 through 152 Processing helix chain 'L' and resid 160 through 174 Processing helix chain 'M' and resid 53 through 71 Processing helix chain 'M' and resid 77 through 92 Processing helix chain 'M' and resid 136 through 145 Processing helix chain 'M' and resid 153 through 170 Processing helix chain 'N' and resid 3 through 7 removed outlier: 3.546A pdb=" N LEU N 7 " --> pdb=" O LEU N 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 3 through 7' Processing helix chain 'N' and resid 108 through 129 Processing helix chain 'N' and resid 135 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 191 through 200 Processing helix chain 'N' and resid 208 through 222 Processing helix chain 'O' and resid 86 through 107 Processing helix chain 'O' and resid 113 through 126 Processing helix chain 'O' and resid 196 through 210 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= A, 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= B, first strand: chain 'A' and resid 73 through 78 removed outlier: 3.755A pdb=" N SER A 133 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing sheet with id= C, 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= D, 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= E, 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= F, 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= G, 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= H, 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= I, 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) removed outlier: 3.883A pdb=" N ASN E 152 " --> pdb=" O CYS E 148 " (cutoff:3.500A) Processing sheet with id= J, 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) Processing sheet with id= K, first strand: chain 'F' and resid 158 through 160 removed outlier: 3.600A pdb=" N TYR F 159 " --> pdb=" O MET F 151 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE F 136 " --> pdb=" O ILE F 152 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY F 139 " --> pdb=" O GLY F 75 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL F 74 " --> pdb=" O ASP F 71 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASP F 71 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N MET F 76 " --> pdb=" O ASN F 69 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ASN F 69 " --> pdb=" O MET F 76 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL F 78 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU F 67 " --> pdb=" O VAL F 78 " (cutoff:3.500A) Processing sheet with id= L, 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= M, first strand: chain 'G' and resid 160 through 163 removed outlier: 4.524A pdb=" N VAL G 151 " --> pdb=" O PHE G 163 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY G 148 " --> pdb=" O ASP G 144 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N CYS G 78 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LYS G 71 " --> pdb=" O CYS G 78 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N MET G 80 " --> pdb=" O LEU G 69 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU G 69 " --> pdb=" O MET G 80 " (cutoff:3.500A) Processing sheet with id= N, 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: 6.432A pdb=" N GLN I 136 " --> pdb=" O CYS I 121 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N PHE I 123 " --> pdb=" O LEU I 134 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU I 134 " --> pdb=" O PHE I 123 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N HIS I 125 " --> pdb=" O VAL I 132 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL I 132 " --> pdb=" O HIS I 125 " (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= O, first strand: chain 'J' and resid 2 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: 3.857A pdb=" N LEU J 85 " --> pdb=" O LEU J 80 " (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: 6.142A pdb=" N ARG J 117 " --> pdb=" O LEU J 17 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N MET J 19 " --> pdb=" O ARG J 117 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE J 119 " --> pdb=" O MET J 19 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU J 205 " --> pdb=" O ARG J 140 " (cutoff:3.500A) Processing sheet with id= P, 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= Q, first strand: chain 'K' and resid 161 through 164 removed outlier: 3.960A pdb=" N SER K 161 " --> pdb=" O TYR K 157 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N CYS K 86 " --> pdb=" O PHE K 79 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N PHE K 79 " --> pdb=" O CYS K 86 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'L' and resid 136 through 140 removed outlier: 3.750A pdb=" N VAL L 20 " --> pdb=" O ILE L 190 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE L 190 " --> pdb=" O VAL L 20 " (cutoff:3.500A) Processing sheet with id= S, 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= T, first strand: chain 'M' and resid 129 through 132 Processing sheet with id= U, 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= V, 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= W, first strand: chain 'N' and resid 92 through 94 removed outlier: 4.356A pdb=" N LYS N 92 " --> pdb=" O MET N 104 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N MET N 159 " --> pdb=" O THR N 103 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'O' and resid 40 through 43 removed outlier: 3.924A pdb=" N VAL O 51 " --> pdb=" O CYS O 224 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'O' and resid 159 through 161 removed outlier: 3.752A pdb=" N GLN O 159 " --> pdb=" O SER O 151 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL O 149 " --> pdb=" O ASP O 161 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR O 78 " --> pdb=" O THR O 75 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR O 75 " --> pdb=" O THR O 78 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE O 80 " --> pdb=" O LYS O 73 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LYS O 73 " --> pdb=" O ILE O 80 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N CYS O 82 " --> pdb=" O CYS O 71 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N CYS O 71 " --> pdb=" O CYS O 82 " (cutoff:3.500A) 1100 hydrogen bonds defined for protein. 3177 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: 7.56 Time building geometry restraints manager: 9.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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: 2033 2.74 - 3.28: 22216 3.28 - 3.82: 37081 3.82 - 4.36: 42019 4.36 - 4.90: 79073 Nonbonded interactions: 182422 Sorted by model distance: nonbonded pdb=" OH TYR G 23 " pdb=" OD1 ASP J 131 " model vdw 2.202 2.440 nonbonded pdb=" O LYS I 275 " pdb=" OG1 THR I 278 " model vdw 2.210 2.440 nonbonded pdb=" OG SER G 17 " pdb=" OD2 ASP J 131 " model vdw 2.235 2.440 nonbonded pdb=" OD1 ASP D 157 " pdb=" OG SER D 159 " model vdw 2.244 2.440 nonbonded pdb=" OG SER A 35 " pdb=" OG SER A 77 " model vdw 2.252 2.440 ... (remaining 182417 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.200 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: 0.020 Extract box with map and model: 7.120 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 62.460 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.080 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:13.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.270 ------------------------------------------------------------------------------- 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= 0.180 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 : 2.899 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: 1.5640 time to fit residues: 578.7340 Evaluate side-chains 253 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 2.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 267 optimal weight: 7.9990 chunk 240 optimal weight: 8.9990 chunk 133 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 248 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 184 optimal weight: 10.0000 chunk 287 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 GLN B 220 ASN ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 GLN F 222 ASN ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 229 GLN L 157 ASN N 237 HIS O 136 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 24654 Z= 0.410 Angle : 0.586 9.041 33451 Z= 0.307 Chirality : 0.045 0.164 3904 Planarity : 0.005 0.053 4270 Dihedral : 4.298 34.583 3480 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.22 % Allowed : 9.07 % Favored : 89.71 % 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: 0.62 (0.15), residues: 3147 helix: 2.57 (0.15), residues: 1135 sheet: 0.15 (0.19), residues: 701 loop : -1.45 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 216 HIS 0.007 0.001 HIS M 132 PHE 0.023 0.002 PHE L 69 TYR 0.037 0.002 TYR B 121 ARG 0.006 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 289 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 259 time to evaluate : 3.091 Fit side-chains REVERT: B 177 GLN cc_start: 0.8518 (tt0) cc_final: 0.8153 (tp-100) REVERT: C 71 MET cc_start: 0.8648 (ttt) cc_final: 0.8380 (ttt) REVERT: C 175 ASN cc_start: 0.8512 (m110) cc_final: 0.8055 (m110) REVERT: D 90 ASP cc_start: 0.8453 (m-30) cc_final: 0.8044 (OUTLIER) REVERT: D 118 ASN cc_start: 0.8644 (OUTLIER) cc_final: 0.8174 (t160) REVERT: E 27 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7393 (tm-30) REVERT: L 12 MET cc_start: 0.8294 (ttt) cc_final: 0.7690 (ttt) REVERT: L 192 LYS cc_start: 0.8919 (tmtt) cc_final: 0.8439 (tptm) REVERT: M 28 MET cc_start: 0.8501 (pmm) cc_final: 0.8261 (pmt) outliers start: 30 outliers final: 14 residues processed: 275 average time/residue: 1.5093 time to fit residues: 472.1487 Evaluate side-chains 256 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 241 time to evaluate : 3.172 ------------------------------------------------------------------------------- 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 118 ASN Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 208 ILE Chi-restraints excluded: chain H residue 45 SER 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 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: 317 random chunks: chunk 159 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 239 optimal weight: 6.9990 chunk 196 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 288 optimal weight: 5.9990 chunk 311 optimal weight: 10.0000 chunk 256 optimal weight: 0.9990 chunk 285 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 231 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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** ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 157 ASN N 144 ASN O 136 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24654 Z= 0.176 Angle : 0.480 7.969 33451 Z= 0.254 Chirality : 0.041 0.167 3904 Planarity : 0.004 0.051 4270 Dihedral : 4.071 34.748 3480 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.38 % Allowed : 11.18 % Favored : 87.44 % 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: 2.69 (0.16), residues: 1135 sheet: 0.35 (0.19), residues: 715 loop : -1.36 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 216 HIS 0.004 0.000 HIS M 132 PHE 0.015 0.001 PHE L 69 TYR 0.017 0.001 TYR O 158 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 303 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 269 time to evaluate : 2.941 Fit side-chains REVERT: B 177 GLN cc_start: 0.8497 (tt0) cc_final: 0.8157 (tp-100) REVERT: C 71 MET cc_start: 0.8612 (ttt) cc_final: 0.8378 (ttt) REVERT: C 175 ASN cc_start: 0.8451 (m110) cc_final: 0.7986 (m110) REVERT: F 114 ASP cc_start: 0.7626 (m-30) cc_final: 0.7304 (m-30) REVERT: H 62 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7953 (tpt) REVERT: I 265 ASN cc_start: 0.7253 (t0) cc_final: 0.6798 (t0) REVERT: J 50 ASP cc_start: 0.8394 (p0) cc_final: 0.8167 (p0) REVERT: K 96 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7392 (m-30) REVERT: L 134 ASP cc_start: 0.8259 (t0) cc_final: 0.7915 (t0) REVERT: L 192 LYS cc_start: 0.8897 (tmtt) cc_final: 0.8394 (tptm) REVERT: M 28 MET cc_start: 0.8507 (pmm) cc_final: 0.8210 (pmt) outliers start: 34 outliers final: 13 residues processed: 286 average time/residue: 1.4897 time to fit residues: 486.3344 Evaluate side-chains 262 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 247 time to evaluate : 2.923 ------------------------------------------------------------------------------- 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 107 MET Chi-restraints excluded: chain D residue 165 CYS 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 K residue 96 ASP Chi-restraints excluded: chain L residue 135 ASP Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 161 ASP Chi-restraints excluded: chain N residue 62 THR Chi-restraints excluded: chain O residue 113 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 284 optimal weight: 3.9990 chunk 216 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 193 optimal weight: 20.0000 chunk 289 optimal weight: 9.9990 chunk 306 optimal weight: 20.0000 chunk 151 optimal weight: 4.9990 chunk 274 optimal weight: 0.0980 chunk 82 optimal weight: 0.4980 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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** ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 186 ASN O 136 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1108 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= 0.202 Angle : 0.483 8.002 33451 Z= 0.255 Chirality : 0.041 0.160 3904 Planarity : 0.004 0.051 4270 Dihedral : 3.998 36.117 3480 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.74 % Allowed : 12.27 % Favored : 85.99 % 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: 0.88 (0.15), residues: 3147 helix: 2.73 (0.16), residues: 1130 sheet: 0.36 (0.19), residues: 709 loop : -1.30 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 216 HIS 0.004 0.001 HIS I 125 PHE 0.016 0.001 PHE L 69 TYR 0.020 0.001 TYR B 121 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 295 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 252 time to evaluate : 2.989 Fit side-chains REVERT: B 177 GLN cc_start: 0.8496 (tt0) cc_final: 0.8157 (tp-100) REVERT: C 71 MET cc_start: 0.8621 (ttt) cc_final: 0.8382 (ttt) REVERT: C 175 ASN cc_start: 0.8442 (m110) cc_final: 0.7972 (m110) REVERT: F 114 ASP cc_start: 0.7605 (m-30) cc_final: 0.7281 (m-30) REVERT: H 62 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7953 (tpt) REVERT: I 265 ASN cc_start: 0.7370 (t0) cc_final: 0.6917 (t0) REVERT: J 50 ASP cc_start: 0.8411 (p0) cc_final: 0.8166 (p0) REVERT: J 83 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.7598 (mtm180) REVERT: K 96 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.7391 (m-30) REVERT: L 134 ASP cc_start: 0.8246 (t70) cc_final: 0.7884 (t0) REVERT: L 192 LYS cc_start: 0.8898 (tmtt) cc_final: 0.8374 (tptm) REVERT: M 28 MET cc_start: 0.8437 (pmm) cc_final: 0.8175 (pmt) REVERT: M 99 HIS cc_start: 0.8483 (OUTLIER) cc_final: 0.8273 (m-70) REVERT: M 108 ASP cc_start: 0.8359 (t0) cc_final: 0.8126 (t0) outliers start: 43 outliers final: 11 residues processed: 283 average time/residue: 1.4492 time to fit residues: 470.3292 Evaluate side-chains 260 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 245 time to evaluate : 3.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain E residue 229 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 135 ASP Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain M residue 11 ASP Chi-restraints excluded: chain M residue 99 HIS Chi-restraints excluded: chain O residue 113 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 255 optimal weight: 7.9990 chunk 173 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 228 optimal weight: 0.6980 chunk 126 optimal weight: 6.9990 chunk 261 optimal weight: 4.9990 chunk 211 optimal weight: 0.4980 chunk 0 optimal weight: 8.9990 chunk 156 optimal weight: 5.9990 chunk 275 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 98 ASN H 58 ASN M 186 ASN O 136 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24654 Z= 0.252 Angle : 0.502 8.164 33451 Z= 0.264 Chirality : 0.041 0.156 3904 Planarity : 0.004 0.051 4270 Dihedral : 4.068 37.294 3480 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.15 % Allowed : 13.28 % Favored : 84.57 % 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: 0.84 (0.15), residues: 3147 helix: 2.68 (0.16), residues: 1129 sheet: 0.39 (0.19), residues: 702 loop : -1.32 (0.16), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 216 HIS 0.005 0.001 HIS I 125 PHE 0.019 0.001 PHE L 69 TYR 0.023 0.001 TYR B 121 ARG 0.009 0.000 ARG I 38 *********************** 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 304 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 251 time to evaluate : 2.994 Fit side-chains REVERT: B 177 GLN cc_start: 0.8490 (tt0) cc_final: 0.8154 (tp-100) REVERT: C 71 MET cc_start: 0.8601 (ttt) cc_final: 0.8385 (ttt) REVERT: C 175 ASN cc_start: 0.8468 (m110) cc_final: 0.7972 (m110) REVERT: E 27 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7419 (tm-30) REVERT: F 114 ASP cc_start: 0.7623 (m-30) cc_final: 0.7309 (m-30) REVERT: G 232 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8179 (mm-30) REVERT: H 62 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7956 (tpt) REVERT: I 265 ASN cc_start: 0.7385 (t0) cc_final: 0.6901 (t0) REVERT: J 50 ASP cc_start: 0.8435 (p0) cc_final: 0.8172 (p0) REVERT: K 96 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7425 (m-30) REVERT: L 134 ASP cc_start: 0.8261 (t70) cc_final: 0.7868 (t0) REVERT: L 192 LYS cc_start: 0.8907 (tmtt) cc_final: 0.8383 (tptm) REVERT: M 99 HIS cc_start: 0.8534 (OUTLIER) cc_final: 0.8241 (m-70) REVERT: M 108 ASP cc_start: 0.8392 (t0) cc_final: 0.8124 (t0) outliers start: 53 outliers final: 23 residues processed: 287 average time/residue: 1.4462 time to fit residues: 475.3390 Evaluate side-chains 269 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 241 time to evaluate : 3.068 ------------------------------------------------------------------------------- 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 97 THR Chi-restraints excluded: chain C residue 98 VAL 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 G residue 112 ASP 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 I residue 285 ASN Chi-restraints excluded: chain J residue 24 VAL 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 M residue 99 HIS Chi-restraints excluded: chain M residue 132 HIS Chi-restraints excluded: chain N residue 62 THR Chi-restraints excluded: chain N residue 198 MET Chi-restraints excluded: chain O residue 113 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 103 optimal weight: 0.3980 chunk 275 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 179 optimal weight: 0.0170 chunk 75 optimal weight: 1.9990 chunk 306 optimal weight: 5.9990 chunk 254 optimal weight: 0.7980 chunk 142 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 186 ASN O 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24654 Z= 0.124 Angle : 0.454 7.703 33451 Z= 0.240 Chirality : 0.040 0.189 3904 Planarity : 0.004 0.049 4270 Dihedral : 3.816 35.680 3480 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.34 % Allowed : 14.58 % Favored : 84.08 % 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: 1.03 (0.15), residues: 3147 helix: 2.88 (0.16), residues: 1112 sheet: 0.52 (0.19), residues: 708 loop : -1.22 (0.16), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 216 HIS 0.004 0.000 HIS I 125 PHE 0.013 0.001 PHE K 207 TYR 0.013 0.001 TYR K 51 ARG 0.010 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 294 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 261 time to evaluate : 3.016 Fit side-chains revert: symmetry clash REVERT: B 177 GLN cc_start: 0.8480 (tt0) cc_final: 0.8163 (tp-100) REVERT: C 71 MET cc_start: 0.8630 (ttt) cc_final: 0.8400 (ttt) REVERT: C 175 ASN cc_start: 0.8395 (m110) cc_final: 0.7918 (m110) REVERT: F 114 ASP cc_start: 0.7552 (m-30) cc_final: 0.7216 (m-30) REVERT: H 62 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7946 (tpt) REVERT: H 68 ARG cc_start: 0.8566 (tmt-80) cc_final: 0.8282 (tmt170) REVERT: I 265 ASN cc_start: 0.7363 (t0) cc_final: 0.6889 (t0) REVERT: J 50 ASP cc_start: 0.8396 (p0) cc_final: 0.8149 (p0) REVERT: L 134 ASP cc_start: 0.8223 (t70) cc_final: 0.7723 (t0) REVERT: L 192 LYS cc_start: 0.8879 (tmtt) cc_final: 0.8346 (tptm) REVERT: M 99 HIS cc_start: 0.8495 (OUTLIER) cc_final: 0.8200 (m-70) REVERT: M 108 ASP cc_start: 0.8374 (t0) cc_final: 0.8118 (t0) outliers start: 33 outliers final: 16 residues processed: 282 average time/residue: 1.4937 time to fit residues: 481.5305 Evaluate side-chains 265 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 247 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain D residue 47 CYS Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 277 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 L residue 150 CYS Chi-restraints excluded: chain L residue 173 ASN Chi-restraints excluded: chain M residue 99 HIS Chi-restraints excluded: chain M residue 132 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 295 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 174 optimal weight: 0.9990 chunk 223 optimal weight: 5.9990 chunk 173 optimal weight: 0.0770 chunk 258 optimal weight: 7.9990 chunk 171 optimal weight: 5.9990 chunk 305 optimal weight: 7.9990 chunk 191 optimal weight: 8.9990 chunk 186 optimal weight: 8.9990 chunk 141 optimal weight: 5.9990 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 186 ASN O 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 24654 Z= 0.328 Angle : 0.539 10.144 33451 Z= 0.282 Chirality : 0.043 0.159 3904 Planarity : 0.004 0.050 4270 Dihedral : 4.124 40.717 3480 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.86 % Allowed : 15.03 % Favored : 83.11 % 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: 2.64 (0.16), residues: 1129 sheet: 0.44 (0.19), residues: 706 loop : -1.33 (0.16), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 216 HIS 0.005 0.001 HIS I 125 PHE 0.023 0.001 PHE L 69 TYR 0.027 0.001 TYR B 121 ARG 0.011 0.000 ARG N 217 *********************** 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 292 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 246 time to evaluate : 2.941 Fit side-chains REVERT: B 177 GLN cc_start: 0.8511 (tt0) cc_final: 0.8173 (tp-100) REVERT: C 175 ASN cc_start: 0.8458 (m110) cc_final: 0.7910 (m110) REVERT: E 27 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7423 (tm-30) REVERT: E 203 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7450 (mm-40) REVERT: F 114 ASP cc_start: 0.7649 (m-30) cc_final: 0.7326 (m-30) REVERT: I 265 ASN cc_start: 0.7373 (t0) cc_final: 0.6904 (t0) REVERT: J 50 ASP cc_start: 0.8383 (p0) cc_final: 0.8120 (p0) REVERT: K 96 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7450 (m-30) REVERT: L 134 ASP cc_start: 0.8253 (t70) cc_final: 0.7820 (t0) REVERT: L 192 LYS cc_start: 0.8923 (tmtt) cc_final: 0.8390 (tptm) REVERT: M 28 MET cc_start: 0.8463 (pmm) cc_final: 0.8073 (pmm) REVERT: M 99 HIS cc_start: 0.8586 (OUTLIER) cc_final: 0.8252 (m-70) REVERT: M 108 ASP cc_start: 0.8456 (t0) cc_final: 0.8142 (t0) outliers start: 46 outliers final: 22 residues processed: 279 average time/residue: 1.4886 time to fit residues: 474.4812 Evaluate side-chains 265 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 239 time to evaluate : 2.906 ------------------------------------------------------------------------------- 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 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 G residue 112 ASP Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 277 MET Chi-restraints excluded: chain I residue 285 ASN Chi-restraints excluded: chain J residue 24 VAL 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 189 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 182 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 240 optimal weight: 8.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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: 0.8406 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24654 Z= 0.148 Angle : 0.473 8.450 33451 Z= 0.250 Chirality : 0.040 0.154 3904 Planarity : 0.004 0.049 4270 Dihedral : 3.918 40.445 3480 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.26 % Allowed : 15.92 % 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: 0.97 (0.15), residues: 3147 helix: 2.76 (0.16), residues: 1122 sheet: 0.55 (0.19), residues: 703 loop : -1.26 (0.16), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 216 HIS 0.005 0.000 HIS I 125 PHE 0.012 0.001 PHE K 207 TYR 0.015 0.001 TYR K 51 ARG 0.012 0.000 ARG N 217 *********************** 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 282 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 251 time to evaluate : 3.013 Fit side-chains REVERT: B 151 ASP cc_start: 0.8277 (t0) cc_final: 0.7796 (t0) REVERT: B 177 GLN cc_start: 0.8472 (tt0) cc_final: 0.8157 (tp-100) REVERT: C 175 ASN cc_start: 0.8394 (m110) cc_final: 0.7872 (m110) REVERT: E 27 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7452 (tm-30) REVERT: E 203 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7424 (mm-40) REVERT: F 114 ASP cc_start: 0.7594 (m-30) cc_final: 0.7267 (m-30) REVERT: I 265 ASN cc_start: 0.7325 (t0) cc_final: 0.6839 (t0) REVERT: J 50 ASP cc_start: 0.8365 (p0) cc_final: 0.8099 (p0) REVERT: L 134 ASP cc_start: 0.8215 (t70) cc_final: 0.7766 (t0) REVERT: L 192 LYS cc_start: 0.8885 (tmtt) cc_final: 0.8342 (tptm) REVERT: M 28 MET cc_start: 0.8404 (pmm) cc_final: 0.7959 (pmm) REVERT: M 99 HIS cc_start: 0.8533 (OUTLIER) cc_final: 0.8147 (m-70) REVERT: M 108 ASP cc_start: 0.8390 (t0) cc_final: 0.8100 (t0) outliers start: 31 outliers final: 19 residues processed: 276 average time/residue: 1.4886 time to fit residues: 469.8023 Evaluate side-chains 263 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 241 time to evaluate : 3.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain B residue 15 GLU 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 G residue 112 ASP Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 277 MET Chi-restraints excluded: chain I residue 285 ASN 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 277 optimal weight: 5.9990 chunk 292 optimal weight: 0.5980 chunk 267 optimal weight: 9.9990 chunk 284 optimal weight: 10.0000 chunk 171 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 223 optimal weight: 0.2980 chunk 87 optimal weight: 0.9990 chunk 257 optimal weight: 0.0570 chunk 269 optimal weight: 9.9990 chunk 283 optimal weight: 3.9990 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 186 ASN O 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24654 Z= 0.145 Angle : 0.481 12.249 33451 Z= 0.250 Chirality : 0.040 0.238 3904 Planarity : 0.004 0.055 4270 Dihedral : 3.816 40.418 3480 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.09 % Allowed : 16.04 % Favored : 82.87 % 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: 1.03 (0.15), residues: 3147 helix: 2.82 (0.16), residues: 1122 sheet: 0.57 (0.19), residues: 711 loop : -1.22 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 216 HIS 0.004 0.000 HIS I 125 PHE 0.013 0.001 PHE L 69 TYR 0.016 0.001 TYR K 51 ARG 0.015 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 277 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 250 time to evaluate : 2.911 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 151 ASP cc_start: 0.8136 (t0) cc_final: 0.7708 (t0) REVERT: B 177 GLN cc_start: 0.8464 (tt0) cc_final: 0.8150 (tp-100) REVERT: C 175 ASN cc_start: 0.8377 (m110) cc_final: 0.7847 (m110) REVERT: E 27 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7458 (tm-30) REVERT: E 203 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7342 (mm-40) REVERT: F 114 ASP cc_start: 0.7580 (m-30) cc_final: 0.7243 (m-30) REVERT: I 265 ASN cc_start: 0.7300 (t0) cc_final: 0.6819 (t0) REVERT: J 50 ASP cc_start: 0.8339 (p0) cc_final: 0.8089 (p0) REVERT: L 134 ASP cc_start: 0.8236 (t70) cc_final: 0.7716 (t0) REVERT: L 192 LYS cc_start: 0.8887 (tmtt) cc_final: 0.8344 (tptm) REVERT: M 28 MET cc_start: 0.8575 (pmm) cc_final: 0.8109 (pmm) REVERT: M 99 HIS cc_start: 0.8535 (OUTLIER) cc_final: 0.8149 (m-70) REVERT: M 108 ASP cc_start: 0.8406 (t0) cc_final: 0.8118 (t0) outliers start: 27 outliers final: 17 residues processed: 273 average time/residue: 1.5031 time to fit residues: 468.4236 Evaluate side-chains 264 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 244 time to evaluate : 3.032 ------------------------------------------------------------------------------- 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 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 G residue 112 ASP Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 285 ASN 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 186 optimal weight: 8.9990 chunk 301 optimal weight: 40.0000 chunk 183 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 209 optimal weight: 0.9990 chunk 315 optimal weight: 20.0000 chunk 290 optimal weight: 9.9990 chunk 251 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 194 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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: 0.8429 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24654 Z= 0.231 Angle : 0.505 9.719 33451 Z= 0.265 Chirality : 0.041 0.170 3904 Planarity : 0.004 0.060 4270 Dihedral : 3.934 37.648 3480 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.22 % Allowed : 16.12 % Favored : 82.67 % 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: 0.98 (0.15), residues: 3147 helix: 2.76 (0.16), residues: 1123 sheet: 0.56 (0.19), residues: 708 loop : -1.26 (0.16), residues: 1316 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 0.018 0.001 PHE L 69 TYR 0.025 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 275 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 245 time to evaluate : 2.757 Fit side-chains revert: symmetry clash REVERT: B 151 ASP cc_start: 0.8293 (t0) cc_final: 0.8054 (t0) REVERT: B 177 GLN cc_start: 0.8488 (tt0) cc_final: 0.8168 (tp-100) REVERT: C 175 ASN cc_start: 0.8402 (m110) cc_final: 0.7861 (m110) REVERT: E 27 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7449 (tm-30) REVERT: E 203 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7380 (mm-40) REVERT: F 114 ASP cc_start: 0.7634 (m-30) cc_final: 0.7306 (m-30) REVERT: I 265 ASN cc_start: 0.7362 (t0) cc_final: 0.6907 (t0) REVERT: J 50 ASP cc_start: 0.8347 (p0) cc_final: 0.8092 (p0) REVERT: L 134 ASP cc_start: 0.8243 (t70) cc_final: 0.7807 (t0) REVERT: L 192 LYS cc_start: 0.8891 (tmtt) cc_final: 0.8344 (tptm) REVERT: M 28 MET cc_start: 0.8576 (pmm) cc_final: 0.8164 (pmm) REVERT: M 99 HIS cc_start: 0.8560 (OUTLIER) cc_final: 0.8213 (m-70) REVERT: M 108 ASP cc_start: 0.8430 (t0) cc_final: 0.8120 (t0) outliers start: 30 outliers final: 20 residues processed: 268 average time/residue: 1.5338 time to fit residues: 472.4271 Evaluate side-chains 263 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 240 time to evaluate : 3.001 ------------------------------------------------------------------------------- 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 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 G residue 112 ASP Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 277 MET Chi-restraints excluded: chain I residue 285 ASN 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 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 O residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 199 optimal weight: 3.9990 chunk 267 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 231 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 69 optimal weight: 0.0570 chunk 251 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 258 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 overall best weight: 2.3704 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.095253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.066183 restraints weight = 47200.805| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.87 r_work: 0.2759 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1391 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= 0.220 Angle : 0.512 12.915 33451 Z= 0.266 Chirality : 0.041 0.155 3904 Planarity : 0.004 0.059 4270 Dihedral : 3.952 35.643 3480 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.22 % Allowed : 16.04 % Favored : 82.75 % 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: 0.96 (0.15), residues: 3147 helix: 2.73 (0.16), residues: 1121 sheet: 0.57 (0.19), residues: 708 loop : -1.26 (0.16), residues: 1318 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 0.027 0.001 TYR K 51 ARG 0.022 0.000 ARG N 217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7985.25 seconds wall clock time: 144 minutes 9.17 seconds (8649.17 seconds total)