Starting phenix.real_space_refine on Sat Mar 16 15:46:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adp_11733/03_2024/7adp_11733.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adp_11733/03_2024/7adp_11733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adp_11733/03_2024/7adp_11733.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adp_11733/03_2024/7adp_11733.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adp_11733/03_2024/7adp_11733.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adp_11733/03_2024/7adp_11733.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.073 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 60 5.16 5 C 9643 2.51 5 N 2580 2.21 5 O 2743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A ASP 265": "OD1" <-> "OD2" Residue "A ASP 285": "OD1" <-> "OD2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A ARG 401": "NH1" <-> "NH2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 420": "NH1" <-> "NH2" Residue "A ARG 445": "NH1" <-> "NH2" Residue "A ASP 459": "OD1" <-> "OD2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A ASP 567": "OD1" <-> "OD2" Residue "A TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 660": "NH1" <-> "NH2" Residue "A ARG 680": "NH1" <-> "NH2" Residue "A ARG 685": "NH1" <-> "NH2" Residue "A ARG 687": "NH1" <-> "NH2" Residue "A TYR 733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 822": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 907": "OE1" <-> "OE2" Residue "A TYR 938": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 953": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 31": "NH1" <-> "NH2" Residue "C ASP 51": "OD1" <-> "OD2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C ASP 85": "OD1" <-> "OD2" Residue "C ARG 147": "NH1" <-> "NH2" Residue "D PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 81": "NH1" <-> "NH2" Residue "H ASP 84": "OD1" <-> "OD2" Residue "H TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 128": "OD1" <-> "OD2" Residue "H ARG 152": "NH1" <-> "NH2" Residue "H ASP 155": "OD1" <-> "OD2" Residue "H ASP 176": "OD1" <-> "OD2" Residue "H ARG 178": "NH1" <-> "NH2" Residue "I ARG 71": "NH1" <-> "NH2" Residue "I ASP 80": "OD1" <-> "OD2" Residue "I ARG 99": "NH1" <-> "NH2" Residue "I ARG 111": "NH1" <-> "NH2" Residue "I ARG 115": "NH1" <-> "NH2" Residue "I ARG 169": "NH1" <-> "NH2" Residue "I GLU 172": "OE1" <-> "OE2" Residue "I ASP 175": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15026 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 881, 6983 Classifications: {'peptide': 881} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 41, 'TRANS': 839} Chain breaks: 7 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2249 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 4, 'TRANS': 268} Chain breaks: 1 Chain: "C" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1562 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 353 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 39} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 726 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain breaks: 1 Chain: "F" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 781 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "H" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1304 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 158} Chain breaks: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1026 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 126} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.71, per 1000 atoms: 0.51 Number of scatterers: 15026 At special positions: 0 Unit cell: (157.536, 141.126, 173.946, 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 60 16.00 O 2743 8.00 N 2580 7.00 C 9643 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 368 " distance=2.03 Simple disulfide: pdb=" SG CYS I 135 " - pdb=" SG CYS I 168 " distance=2.04 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 Links applied NAG-ASN " NAG A1001 " - " ASN A 370 " " NAG A1002 " - " ASN A 818 " " NAG I 301 " - " ASN I 182 " Time building additional restraints: 5.07 Conformation dependent library (CDL) restraints added in 2.4 seconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3544 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 26 sheets defined 37.6% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 482 through 502 removed outlier: 3.599A pdb=" N LEU A 502 " --> pdb=" O TRP A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 666 Processing helix chain 'A' and resid 876 through 879 removed outlier: 3.657A pdb=" N ASP A 879 " --> pdb=" O ALA A 876 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 876 through 879' Processing helix chain 'A' and resid 962 through 992 removed outlier: 4.171A pdb=" N SER A 966 " --> pdb=" O TYR A 962 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ARG A 981 " --> pdb=" O MET A 977 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 982 " --> pdb=" O ILE A 978 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 985 " --> pdb=" O ARG A 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 25 removed outlier: 3.813A pdb=" N TRP B 22 " --> pdb=" O LYS B 18 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG B 23 " --> pdb=" O MET B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 44 removed outlier: 4.674A pdb=" N GLU B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 49 removed outlier: 3.581A pdb=" N GLY B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 59 Processing helix chain 'B' and resid 59 through 67 removed outlier: 4.550A pdb=" N ASP B 65 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 83 removed outlier: 3.797A pdb=" N PHE B 74 " --> pdb=" O ASP B 70 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU B 78 " --> pdb=" O PHE B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 100 removed outlier: 3.665A pdb=" N LEU B 92 " --> pdb=" O ARG B 88 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG B 96 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU B 98 " --> pdb=" O GLY B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 117 removed outlier: 3.709A pdb=" N ALA B 106 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 135 removed outlier: 3.606A pdb=" N ARG B 131 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 151 removed outlier: 3.644A pdb=" N ALA B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 168 removed outlier: 4.065A pdb=" N GLU B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 182 removed outlier: 3.512A pdb=" N CYS B 177 " --> pdb=" O LYS B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 201 removed outlier: 4.147A pdb=" N CYS B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 223 removed outlier: 3.728A pdb=" N LEU B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 240 Processing helix chain 'B' and resid 246 through 272 removed outlier: 3.555A pdb=" N GLY B 272 " --> pdb=" O TYR B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 292 removed outlier: 4.321A pdb=" N LEU B 292 " --> pdb=" O MET B 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 39 removed outlier: 3.866A pdb=" N ARG C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Proline residue: C 19 - end of helix Processing helix chain 'C' and resid 46 through 64 Processing helix chain 'C' and resid 69 through 82 removed outlier: 3.627A pdb=" N PHE C 73 " --> pdb=" O PRO C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 145 through 147 No H-bonds generated for 'chain 'C' and resid 145 through 147' Processing helix chain 'C' and resid 148 through 153 removed outlier: 3.617A pdb=" N LEU C 152 " --> pdb=" O PHE C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 187 removed outlier: 3.965A pdb=" N PHE C 177 " --> pdb=" O PHE C 173 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N SER C 184 " --> pdb=" O ARG C 180 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU C 185 " --> pdb=" O SER C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 227 removed outlier: 3.667A pdb=" N LEU C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 243 Processing helix chain 'D' and resid 161 through 166 Processing helix chain 'E' and resid 5 through 34 Processing helix chain 'E' and resid 43 through 64 removed outlier: 3.676A pdb=" N GLY E 59 " --> pdb=" O VAL E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 76 removed outlier: 4.076A pdb=" N GLU E 75 " --> pdb=" O ASP E 71 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU E 76 " --> pdb=" O ALA E 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 71 through 76' Processing helix chain 'E' and resid 77 through 79 No H-bonds generated for 'chain 'E' and resid 77 through 79' Processing helix chain 'E' and resid 80 through 86 removed outlier: 3.576A pdb=" N LEU E 84 " --> pdb=" O THR E 80 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN E 86 " --> pdb=" O ASP E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 95 through 100 removed outlier: 3.501A pdb=" N ARG E 98 " --> pdb=" O HIS E 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 44 removed outlier: 4.258A pdb=" N LEU F 44 " --> pdb=" O THR F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 71 Processing helix chain 'F' and resid 81 through 86 removed outlier: 3.662A pdb=" N PHE F 85 " --> pdb=" O ARG F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 109 removed outlier: 3.764A pdb=" N LEU F 93 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE F 94 " --> pdb=" O ILE F 90 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR F 95 " --> pdb=" O GLY F 91 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL F 109 " --> pdb=" O GLY F 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 21 removed outlier: 3.507A pdb=" N TYR H 21 " --> pdb=" O HIS H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 85 removed outlier: 4.225A pdb=" N LEU H 71 " --> pdb=" O LEU H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 120 Processing helix chain 'H' and resid 166 through 177 Processing helix chain 'H' and resid 178 through 183 removed outlier: 5.186A pdb=" N GLU H 181 " --> pdb=" O ARG H 178 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU H 183 " --> pdb=" O TYR H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 192 Processing helix chain 'H' and resid 199 through 206 removed outlier: 3.502A pdb=" N ASN H 203 " --> pdb=" O ASN H 199 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL H 206 " --> pdb=" O ILE H 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 104 removed outlier: 3.572A pdb=" N LEU I 104 " --> pdb=" O ASP I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 139 removed outlier: 4.267A pdb=" N GLU I 139 " --> pdb=" O CYS I 135 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 44 removed outlier: 6.917A pdb=" N ALA A 57 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ALA A 43 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL A 55 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA A 64 " --> pdb=" O VAL A 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA3, first strand: chain 'A' and resid 106 through 109 removed outlier: 3.659A pdb=" N TRP A 119 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA5, first strand: chain 'A' and resid 150 through 154 Processing sheet with id=AA6, first strand: chain 'A' and resid 177 through 179 removed outlier: 4.166A pdb=" N MET A 177 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 189 " --> pdb=" O MET A 177 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR A 179 " --> pdb=" O TRP A 187 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A 188 " --> pdb=" O VAL A 200 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 235 through 239 Processing sheet with id=AA8, first strand: chain 'A' and resid 275 through 277 removed outlier: 6.562A pdb=" N HIS A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR A 300 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASN A 315 " --> pdb=" O TYR A 300 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU A 302 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 319 through 326 removed outlier: 7.160A pdb=" N THR A 319 " --> pdb=" O CYS A 338 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N CYS A 338 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU A 321 " --> pdb=" O MET A 336 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA A 325 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 377 " --> pdb=" O THR A 389 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N THR A 389 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 12.117A pdb=" N LEU A 379 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 11.819A pdb=" N LEU A 387 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 406 through 409 removed outlier: 6.593A pdb=" N LEU A 430 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER A 444 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE A 432 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 457 removed outlier: 4.073A pdb=" N CYS A 454 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 544 through 545 Processing sheet with id=AB4, first strand: chain 'A' and resid 570 through 576 removed outlier: 3.682A pdb=" N MET A 573 " --> pdb=" O THR A 588 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 575 " --> pdb=" O GLN A 586 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLN A 586 " --> pdb=" O GLN A 575 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 625 through 627 removed outlier: 4.109A pdb=" N GLN A 625 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 696 through 699 Processing sheet with id=AB7, first strand: chain 'A' and resid 706 through 712 removed outlier: 7.208A pdb=" N VAL A 744 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL A 710 " --> pdb=" O ALA A 742 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA A 742 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLY A 712 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N LEU A 740 " --> pdb=" O GLY A 712 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS A 771 " --> pdb=" O LEU A 761 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ASP A 763 " --> pdb=" O ILE A 769 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A 769 " --> pdb=" O ASP A 763 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N THR I 191 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N SER A 772 " --> pdb=" O THR I 191 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 734 removed outlier: 4.046A pdb=" N GLY A 813 " --> pdb=" O TYR A 733 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS A 783 " --> pdb=" O GLN A 794 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 734 removed outlier: 4.046A pdb=" N GLY A 813 " --> pdb=" O TYR A 733 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 845 through 849 removed outlier: 4.112A pdb=" N ALA A 846 " --> pdb=" O GLY A 864 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 921 through 926 removed outlier: 4.148A pdb=" N GLY A 921 " --> pdb=" O TYR A 938 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A 938 " --> pdb=" O GLY A 921 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N CYS A 933 " --> pdb=" O VAL A 947 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 5 through 6 removed outlier: 7.012A pdb=" N LYS H 5 " --> pdb=" O PHE H 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'H' and resid 56 through 62 removed outlier: 4.000A pdb=" N LEU H 60 " --> pdb=" O ASN H 27 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ASN H 27 " --> pdb=" O LEU H 60 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL H 26 " --> pdb=" O GLN H 94 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLN H 94 " --> pdb=" O VAL H 26 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLY H 28 " --> pdb=" O TYR H 92 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N TYR H 92 " --> pdb=" O GLY H 28 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU H 30 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA H 123 " --> pdb=" O ALA H 90 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 144 through 145 Processing sheet with id=AC6, first strand: chain 'I' and resid 52 through 54 Processing sheet with id=AC7, first strand: chain 'I' and resid 69 through 70 removed outlier: 3.640A pdb=" N ARG I 69 " --> pdb=" O HIS I 58 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 156 through 163 621 hydrogen bonds defined for protein. 1767 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: 4.55 Time building geometry restraints manager: 5.62 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: 4841 1.34 - 1.46: 3411 1.46 - 1.58: 7001 1.58 - 1.70: 0 1.70 - 1.82: 100 Bond restraints: 15353 Sorted by residual: bond pdb=" CG LEU A 54 " pdb=" CD2 LEU A 54 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.55e+00 bond pdb=" CG1 ILE A 863 " pdb=" CD1 ILE A 863 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.35e+00 bond pdb=" C1 NAG A1001 " pdb=" O5 NAG A1001 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 2.99e+00 bond pdb=" C1 NAG A1002 " pdb=" O5 NAG A1002 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.96e+00 bond pdb=" CB THR A 425 " pdb=" CG2 THR A 425 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.23e+00 ... (remaining 15348 not shown) Histogram of bond angle deviations from ideal: 98.63 - 105.97: 304 105.97 - 113.31: 8448 113.31 - 120.65: 6190 120.65 - 127.99: 5681 127.99 - 135.33: 186 Bond angle restraints: 20809 Sorted by residual: angle pdb=" C ASP A 231 " pdb=" N GLU A 232 " pdb=" CA GLU A 232 " ideal model delta sigma weight residual 121.54 128.72 -7.18 1.91e+00 2.74e-01 1.41e+01 angle pdb=" C ARG F 72 " pdb=" N ARG F 73 " pdb=" CA ARG F 73 " ideal model delta sigma weight residual 121.54 128.31 -6.77 1.91e+00 2.74e-01 1.26e+01 angle pdb=" C HIS I 164 " pdb=" N PRO I 165 " pdb=" CA PRO I 165 " ideal model delta sigma weight residual 127.00 135.33 -8.33 2.40e+00 1.74e-01 1.20e+01 angle pdb=" CA TRP F 100 " pdb=" CB TRP F 100 " pdb=" CG TRP F 100 " ideal model delta sigma weight residual 113.60 119.90 -6.30 1.90e+00 2.77e-01 1.10e+01 angle pdb=" CA GLU F 16 " pdb=" CB GLU F 16 " pdb=" CG GLU F 16 " ideal model delta sigma weight residual 114.10 120.38 -6.28 2.00e+00 2.50e-01 9.86e+00 ... (remaining 20804 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 8027 17.51 - 35.03: 920 35.03 - 52.54: 194 52.54 - 70.06: 25 70.06 - 87.57: 14 Dihedral angle restraints: 9180 sinusoidal: 3709 harmonic: 5471 Sorted by residual: dihedral pdb=" CA GLU A 232 " pdb=" C GLU A 232 " pdb=" N ALA A 233 " pdb=" CA ALA A 233 " ideal model delta harmonic sigma weight residual 180.00 139.17 40.83 0 5.00e+00 4.00e-02 6.67e+01 dihedral pdb=" CB CYS I 135 " pdb=" SG CYS I 135 " pdb=" SG CYS I 168 " pdb=" CB CYS I 168 " ideal model delta sinusoidal sigma weight residual 93.00 160.65 -67.65 1 1.00e+01 1.00e-02 5.95e+01 dihedral pdb=" CA PRO H 59 " pdb=" C PRO H 59 " pdb=" N LEU H 60 " pdb=" CA LEU H 60 " ideal model delta harmonic sigma weight residual -180.00 -141.89 -38.11 0 5.00e+00 4.00e-02 5.81e+01 ... (remaining 9177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1543 0.039 - 0.079: 575 0.079 - 0.118: 203 0.118 - 0.157: 39 0.157 - 0.196: 5 Chirality restraints: 2365 Sorted by residual: chirality pdb=" C1 NAG A1001 " pdb=" ND2 ASN A 370 " pdb=" C2 NAG A1001 " pdb=" O5 NAG A1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.64e-01 chirality pdb=" CA GLU F 16 " pdb=" N GLU F 16 " pdb=" C GLU F 16 " pdb=" CB GLU F 16 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CA ILE A 863 " pdb=" N ILE A 863 " pdb=" C ILE A 863 " pdb=" CB ILE A 863 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.87e-01 ... (remaining 2362 not shown) Planarity restraints: 2628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 370 " 0.257 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" CG ASN A 370 " -0.111 2.00e-02 2.50e+03 pdb=" OD1 ASN A 370 " -0.052 2.00e-02 2.50e+03 pdb=" ND2 ASN A 370 " -0.458 2.00e-02 2.50e+03 pdb=" C1 NAG A1001 " 0.364 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 818 " -0.158 2.00e-02 2.50e+03 1.70e-01 3.62e+02 pdb=" CG ASN A 818 " 0.064 2.00e-02 2.50e+03 pdb=" OD1 ASN A 818 " 0.037 2.00e-02 2.50e+03 pdb=" ND2 ASN A 818 " 0.266 2.00e-02 2.50e+03 pdb=" C1 NAG A1002 " -0.209 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 182 " -0.137 2.00e-02 2.50e+03 1.52e-01 2.91e+02 pdb=" CG ASN I 182 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN I 182 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN I 182 " 0.249 2.00e-02 2.50e+03 pdb=" C1 NAG I 301 " -0.181 2.00e-02 2.50e+03 ... (remaining 2625 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 124 2.51 - 3.11: 11979 3.11 - 3.71: 22328 3.71 - 4.30: 29451 4.30 - 4.90: 50394 Nonbonded interactions: 114276 Sorted by model distance: nonbonded pdb=" O GLN A 533 " pdb=" OG SER A 550 " model vdw 1.915 2.440 nonbonded pdb=" O HIS A 751 " pdb=" OG1 THR A 755 " model vdw 1.993 2.440 nonbonded pdb=" OG SER I 136 " pdb=" O GLY I 166 " model vdw 2.080 2.440 nonbonded pdb=" OG1 THR A 857 " pdb=" OG SER A 950 " model vdw 2.088 2.440 nonbonded pdb=" OD1 ASP A 239 " pdb=" OG SER A 241 " model vdw 2.096 2.440 ... (remaining 114271 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 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: 0.010 Extract box with map and model: 6.780 Check model and map are aligned: 0.240 Set scattering table: 0.130 Process input model: 39.290 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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 : 0.006 0.071 15353 Z= 0.423 Angle : 0.791 8.744 20809 Z= 0.428 Chirality : 0.046 0.196 2365 Planarity : 0.005 0.070 2625 Dihedral : 15.291 87.573 5627 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.12 % Allowed : 4.18 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.91 (0.15), residues: 1830 helix: -1.93 (0.17), residues: 617 sheet: -3.06 (0.21), residues: 385 loop : -4.46 (0.14), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 100 HIS 0.009 0.001 HIS A 294 PHE 0.021 0.002 PHE A 292 TYR 0.023 0.002 TYR F 110 ARG 0.010 0.001 ARG F 73 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 227 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 567 ASP cc_start: 0.7982 (m-30) cc_final: 0.7766 (p0) REVERT: B 51 ASP cc_start: 0.8644 (t0) cc_final: 0.8164 (t0) REVERT: B 197 GLU cc_start: 0.8417 (mt-10) cc_final: 0.7958 (mt-10) REVERT: C 31 ARG cc_start: 0.8350 (ttt-90) cc_final: 0.7959 (ptt-90) REVERT: C 39 GLN cc_start: 0.8391 (mt0) cc_final: 0.8118 (tm-30) REVERT: E 71 ASP cc_start: 0.7941 (m-30) cc_final: 0.7594 (m-30) REVERT: E 91 TYR cc_start: 0.8370 (m-10) cc_final: 0.7791 (m-80) REVERT: H 98 ARG cc_start: 0.7382 (mtp180) cc_final: 0.7169 (mtm180) outliers start: 2 outliers final: 1 residues processed: 229 average time/residue: 0.3626 time to fit residues: 113.9960 Evaluate side-chains 141 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 0.7980 chunk 140 optimal weight: 9.9990 chunk 78 optimal weight: 0.3980 chunk 48 optimal weight: 0.0870 chunk 95 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS A 371 GLN ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN A 944 GLN A 989 ASN B 169 HIS B 223 ASN C 154 GLN C 175 ASN ** H 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15353 Z= 0.180 Angle : 0.671 10.658 20809 Z= 0.340 Chirality : 0.046 0.227 2365 Planarity : 0.004 0.055 2625 Dihedral : 5.564 47.932 2096 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 1.23 % Allowed : 12.18 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.18), residues: 1830 helix: 0.35 (0.21), residues: 627 sheet: -2.02 (0.23), residues: 391 loop : -3.68 (0.17), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 219 HIS 0.006 0.001 HIS A 580 PHE 0.016 0.001 PHE A 530 TYR 0.012 0.001 TYR H 21 ARG 0.010 0.001 ARG F 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 172 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 917 SER cc_start: 0.8547 (t) cc_final: 0.7817 (m) REVERT: B 51 ASP cc_start: 0.8664 (t0) cc_final: 0.8090 (t0) REVERT: B 197 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7646 (mp0) REVERT: B 223 ASN cc_start: 0.7438 (OUTLIER) cc_final: 0.6483 (t0) REVERT: C 29 MET cc_start: 0.8222 (tpp) cc_final: 0.7820 (mpp) REVERT: C 31 ARG cc_start: 0.8306 (ttt-90) cc_final: 0.7901 (ptt-90) REVERT: C 219 LYS cc_start: 0.8805 (mmtt) cc_final: 0.8589 (mmtt) REVERT: E 91 TYR cc_start: 0.8529 (m-10) cc_final: 0.7892 (m-80) REVERT: F 16 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8364 (tm-30) REVERT: F 46 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8098 (pp) REVERT: F 106 MET cc_start: 0.8160 (mmm) cc_final: 0.7791 (mmp) REVERT: H 178 ARG cc_start: 0.8403 (mmm-85) cc_final: 0.7968 (tpp80) REVERT: H 195 ASN cc_start: 0.7877 (m-40) cc_final: 0.7220 (t0) REVERT: I 178 LEU cc_start: 0.4284 (OUTLIER) cc_final: 0.3996 (pp) outliers start: 20 outliers final: 12 residues processed: 187 average time/residue: 0.3152 time to fit residues: 83.2885 Evaluate side-chains 153 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 138 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 100 TRP Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain I residue 168 CYS Chi-restraints excluded: chain I residue 178 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 0.0040 chunk 52 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 169 optimal weight: 0.0970 chunk 182 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 167 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS A 435 GLN ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS B 223 ASN C 71 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15353 Z= 0.160 Angle : 0.622 12.886 20809 Z= 0.315 Chirality : 0.043 0.231 2365 Planarity : 0.004 0.048 2625 Dihedral : 5.240 47.518 2096 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 1.91 % Allowed : 15.08 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -1.95 (0.19), residues: 1830 helix: 1.02 (0.21), residues: 633 sheet: -1.35 (0.25), residues: 385 loop : -3.30 (0.18), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 219 HIS 0.005 0.001 HIS B 189 PHE 0.014 0.001 PHE A 530 TYR 0.019 0.001 TYR H 21 ARG 0.008 0.000 ARG C 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 162 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 917 SER cc_start: 0.8565 (t) cc_final: 0.7903 (m) REVERT: B 51 ASP cc_start: 0.8630 (t0) cc_final: 0.7994 (t0) REVERT: B 100 MET cc_start: 0.8570 (mtt) cc_final: 0.8355 (mpp) REVERT: B 197 GLU cc_start: 0.8450 (mt-10) cc_final: 0.7819 (mp0) REVERT: B 223 ASN cc_start: 0.7077 (OUTLIER) cc_final: 0.6480 (t0) REVERT: C 31 ARG cc_start: 0.8322 (ttt-90) cc_final: 0.7882 (ptt-90) REVERT: C 235 ASP cc_start: 0.8435 (p0) cc_final: 0.8032 (m-30) REVERT: C 236 ASP cc_start: 0.8024 (p0) cc_final: 0.7758 (p0) REVERT: E 31 MET cc_start: 0.8248 (mmt) cc_final: 0.8032 (mmm) REVERT: E 91 TYR cc_start: 0.8495 (m-10) cc_final: 0.7843 (m-80) REVERT: F 106 MET cc_start: 0.8306 (mmm) cc_final: 0.7842 (mmp) REVERT: H 21 TYR cc_start: 0.8689 (m-80) cc_final: 0.8404 (m-10) REVERT: H 83 LYS cc_start: 0.8904 (mmtp) cc_final: 0.8693 (mtpt) REVERT: H 178 ARG cc_start: 0.8374 (mmm-85) cc_final: 0.7970 (tpp80) REVERT: H 195 ASN cc_start: 0.7803 (m-40) cc_final: 0.7182 (t0) REVERT: I 178 LEU cc_start: 0.4159 (OUTLIER) cc_final: 0.3897 (pp) outliers start: 31 outliers final: 13 residues processed: 184 average time/residue: 0.2998 time to fit residues: 79.2146 Evaluate side-chains 156 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 141 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain I residue 135 CYS Chi-restraints excluded: chain I residue 168 CYS Chi-restraints excluded: chain I residue 178 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 169 optimal weight: 9.9990 chunk 179 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 160 optimal weight: 8.9990 chunk 48 optimal weight: 0.0980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 HIS B 169 HIS ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15353 Z= 0.196 Angle : 0.609 11.760 20809 Z= 0.309 Chirality : 0.043 0.197 2365 Planarity : 0.004 0.044 2625 Dihedral : 5.066 48.174 2096 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 2.40 % Allowed : 17.05 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -1.57 (0.20), residues: 1830 helix: 1.27 (0.22), residues: 634 sheet: -0.95 (0.26), residues: 393 loop : -3.14 (0.18), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 100 HIS 0.006 0.001 HIS B 189 PHE 0.016 0.001 PHE A 128 TYR 0.013 0.001 TYR H 21 ARG 0.010 0.000 ARG F 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 151 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 917 SER cc_start: 0.8587 (t) cc_final: 0.7985 (m) REVERT: B 51 ASP cc_start: 0.8669 (t0) cc_final: 0.8024 (t0) REVERT: B 100 MET cc_start: 0.8739 (mtt) cc_final: 0.8398 (mpp) REVERT: B 197 GLU cc_start: 0.8550 (mt-10) cc_final: 0.7845 (mp0) REVERT: B 223 ASN cc_start: 0.7246 (OUTLIER) cc_final: 0.6632 (t0) REVERT: C 31 ARG cc_start: 0.8249 (ttt-90) cc_final: 0.7715 (ptt-90) REVERT: E 91 TYR cc_start: 0.8555 (m-10) cc_final: 0.7899 (m-80) REVERT: F 16 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8394 (tm-30) REVERT: F 20 ARG cc_start: 0.7781 (mtm110) cc_final: 0.7536 (mtm110) REVERT: F 106 MET cc_start: 0.8363 (mmm) cc_final: 0.7900 (mmp) REVERT: H 195 ASN cc_start: 0.7865 (m-40) cc_final: 0.7236 (t0) REVERT: I 178 LEU cc_start: 0.4164 (OUTLIER) cc_final: 0.3821 (pp) outliers start: 39 outliers final: 27 residues processed: 184 average time/residue: 0.2876 time to fit residues: 76.9999 Evaluate side-chains 162 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 881 ARG Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain E residue 26 GLN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 147 HIS Chi-restraints excluded: chain I residue 135 CYS Chi-restraints excluded: chain I residue 144 ASP Chi-restraints excluded: chain I residue 168 CYS Chi-restraints excluded: chain I residue 178 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 133 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 161 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN E 87 HIS ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15353 Z= 0.294 Angle : 0.661 12.935 20809 Z= 0.337 Chirality : 0.045 0.192 2365 Planarity : 0.004 0.045 2625 Dihedral : 5.307 47.943 2096 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 3.26 % Allowed : 17.78 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -1.50 (0.20), residues: 1830 helix: 1.32 (0.22), residues: 635 sheet: -0.89 (0.26), residues: 390 loop : -3.10 (0.18), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 100 HIS 0.012 0.001 HIS A 583 PHE 0.019 0.001 PHE A 581 TYR 0.017 0.002 TYR A 817 ARG 0.007 0.000 ARG H 169 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 144 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 HIS cc_start: 0.7818 (t-90) cc_final: 0.7262 (t-90) REVERT: A 917 SER cc_start: 0.8756 (t) cc_final: 0.8147 (m) REVERT: B 51 ASP cc_start: 0.8675 (t0) cc_final: 0.8025 (t0) REVERT: B 100 MET cc_start: 0.8736 (mtt) cc_final: 0.8337 (mpp) REVERT: B 197 GLU cc_start: 0.8580 (mt-10) cc_final: 0.7860 (mp0) REVERT: B 208 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7259 (tt) REVERT: B 223 ASN cc_start: 0.7462 (OUTLIER) cc_final: 0.7051 (t0) REVERT: C 31 ARG cc_start: 0.8296 (ttt-90) cc_final: 0.7770 (ptt-90) REVERT: C 242 MET cc_start: 0.7789 (mmm) cc_final: 0.7568 (mmm) REVERT: E 91 TYR cc_start: 0.8681 (m-10) cc_final: 0.8060 (m-80) REVERT: F 100 TRP cc_start: 0.7918 (OUTLIER) cc_final: 0.7686 (t60) REVERT: F 106 MET cc_start: 0.8371 (mmm) cc_final: 0.7802 (mmp) REVERT: H 195 ASN cc_start: 0.7887 (m-40) cc_final: 0.7288 (t0) REVERT: I 178 LEU cc_start: 0.4440 (OUTLIER) cc_final: 0.3966 (pp) outliers start: 53 outliers final: 40 residues processed: 185 average time/residue: 0.3244 time to fit residues: 86.9323 Evaluate side-chains 179 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 135 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 338 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 881 ARG Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain E residue 26 GLN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 75 ASN Chi-restraints excluded: chain F residue 100 TRP Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 147 HIS Chi-restraints excluded: chain H residue 182 THR Chi-restraints excluded: chain I residue 144 ASP Chi-restraints excluded: chain I residue 168 CYS Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 178 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 3.9990 chunk 161 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 179 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15353 Z= 0.172 Angle : 0.598 14.681 20809 Z= 0.303 Chirality : 0.043 0.190 2365 Planarity : 0.004 0.040 2625 Dihedral : 5.057 49.710 2096 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 2.58 % Allowed : 19.94 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -1.20 (0.20), residues: 1830 helix: 1.50 (0.22), residues: 634 sheet: -0.62 (0.27), residues: 395 loop : -2.94 (0.19), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 100 HIS 0.005 0.001 HIS B 189 PHE 0.011 0.001 PHE C 218 TYR 0.012 0.001 TYR A 672 ARG 0.012 0.000 ARG F 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 146 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 HIS cc_start: 0.7841 (t-90) cc_final: 0.7243 (t-90) REVERT: A 917 SER cc_start: 0.8702 (t) cc_final: 0.8066 (m) REVERT: B 51 ASP cc_start: 0.8631 (t0) cc_final: 0.7992 (t0) REVERT: B 182 MET cc_start: 0.8300 (ttp) cc_final: 0.7980 (ttp) REVERT: B 197 GLU cc_start: 0.8554 (mt-10) cc_final: 0.7819 (mp0) REVERT: B 208 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7212 (tt) REVERT: B 223 ASN cc_start: 0.7606 (OUTLIER) cc_final: 0.6831 (t0) REVERT: C 31 ARG cc_start: 0.8242 (ttt-90) cc_final: 0.7620 (ptt-90) REVERT: C 236 ASP cc_start: 0.8266 (p0) cc_final: 0.7950 (t0) REVERT: C 242 MET cc_start: 0.7832 (mmm) cc_final: 0.7598 (mmm) REVERT: E 91 TYR cc_start: 0.8659 (m-10) cc_final: 0.8060 (m-80) REVERT: F 16 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8281 (tm-30) REVERT: F 106 MET cc_start: 0.8488 (mmm) cc_final: 0.7911 (mmp) REVERT: H 195 ASN cc_start: 0.7904 (m-40) cc_final: 0.7238 (t0) REVERT: I 178 LEU cc_start: 0.4248 (OUTLIER) cc_final: 0.3887 (pp) outliers start: 42 outliers final: 30 residues processed: 181 average time/residue: 0.2933 time to fit residues: 76.9719 Evaluate side-chains 170 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 137 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 881 ARG Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain E residue 26 GLN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 75 ASN Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 147 HIS Chi-restraints excluded: chain I residue 135 CYS Chi-restraints excluded: chain I residue 178 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 131 optimal weight: 0.4980 chunk 101 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 179 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN B 238 HIS ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 188 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15353 Z= 0.262 Angle : 0.630 13.708 20809 Z= 0.321 Chirality : 0.044 0.181 2365 Planarity : 0.004 0.044 2625 Dihedral : 5.123 50.901 2096 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 3.63 % Allowed : 19.94 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -1.17 (0.20), residues: 1830 helix: 1.51 (0.21), residues: 635 sheet: -0.67 (0.26), residues: 402 loop : -2.88 (0.19), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 100 HIS 0.005 0.001 HIS B 189 PHE 0.015 0.001 PHE A 652 TYR 0.015 0.001 TYR A 943 ARG 0.013 0.000 ARG F 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 145 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 HIS cc_start: 0.7932 (t-90) cc_final: 0.7284 (t-90) REVERT: A 917 SER cc_start: 0.8783 (t) cc_final: 0.8127 (m) REVERT: B 51 ASP cc_start: 0.8645 (t0) cc_final: 0.8001 (t0) REVERT: B 95 MET cc_start: 0.7548 (mmt) cc_final: 0.7327 (mmt) REVERT: B 182 MET cc_start: 0.8395 (ttp) cc_final: 0.8050 (ttp) REVERT: B 197 GLU cc_start: 0.8568 (mt-10) cc_final: 0.7841 (mp0) REVERT: B 223 ASN cc_start: 0.7552 (OUTLIER) cc_final: 0.6904 (t0) REVERT: C 31 ARG cc_start: 0.8242 (ttt-90) cc_final: 0.7625 (ptt-90) REVERT: C 236 ASP cc_start: 0.8376 (p0) cc_final: 0.7903 (t0) REVERT: C 242 MET cc_start: 0.7838 (mmm) cc_final: 0.7606 (mmm) REVERT: E 91 TYR cc_start: 0.8665 (m-10) cc_final: 0.8140 (m-80) REVERT: F 16 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8250 (tm-30) REVERT: H 195 ASN cc_start: 0.7953 (m-40) cc_final: 0.7365 (t0) REVERT: I 178 LEU cc_start: 0.4480 (OUTLIER) cc_final: 0.4055 (pp) outliers start: 59 outliers final: 41 residues processed: 196 average time/residue: 0.2864 time to fit residues: 82.0805 Evaluate side-chains 186 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 143 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 338 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 881 ARG Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 979 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain E residue 26 GLN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 75 ASN Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 147 HIS Chi-restraints excluded: chain I residue 135 CYS Chi-restraints excluded: chain I residue 144 ASP Chi-restraints excluded: chain I residue 178 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 88 optimal weight: 0.2980 chunk 16 optimal weight: 6.9990 chunk 140 optimal weight: 6.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 HIS ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15353 Z= 0.277 Angle : 0.651 14.334 20809 Z= 0.329 Chirality : 0.044 0.181 2365 Planarity : 0.004 0.047 2625 Dihedral : 5.211 52.922 2096 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 3.57 % Allowed : 20.25 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -1.17 (0.20), residues: 1830 helix: 1.48 (0.21), residues: 635 sheet: -0.69 (0.26), residues: 403 loop : -2.84 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 100 HIS 0.005 0.001 HIS A 294 PHE 0.011 0.001 PHE A 530 TYR 0.019 0.001 TYR F 77 ARG 0.008 0.000 ARG H 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 147 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 THR cc_start: 0.8467 (OUTLIER) cc_final: 0.8253 (p) REVERT: A 642 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8904 (mt) REVERT: B 51 ASP cc_start: 0.8655 (t0) cc_final: 0.8011 (t0) REVERT: B 197 GLU cc_start: 0.8580 (mt-10) cc_final: 0.7825 (mp0) REVERT: B 223 ASN cc_start: 0.7492 (OUTLIER) cc_final: 0.6817 (t0) REVERT: C 31 ARG cc_start: 0.8244 (ttt-90) cc_final: 0.7639 (ptt-90) REVERT: C 236 ASP cc_start: 0.8376 (p0) cc_final: 0.7875 (t0) REVERT: C 242 MET cc_start: 0.7839 (mmm) cc_final: 0.7616 (mmm) REVERT: D 43 TYR cc_start: 0.6585 (OUTLIER) cc_final: 0.6144 (t80) REVERT: E 91 TYR cc_start: 0.8688 (m-10) cc_final: 0.8163 (m-80) REVERT: F 106 MET cc_start: 0.8388 (mmm) cc_final: 0.7986 (mmp) REVERT: H 195 ASN cc_start: 0.8096 (m-40) cc_final: 0.7501 (t0) REVERT: I 178 LEU cc_start: 0.4562 (OUTLIER) cc_final: 0.4118 (pp) outliers start: 58 outliers final: 43 residues processed: 195 average time/residue: 0.2725 time to fit residues: 77.7030 Evaluate side-chains 188 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 140 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 338 CYS Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 881 ARG Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 979 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain E residue 26 GLN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 75 ASN Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 147 HIS Chi-restraints excluded: chain I residue 135 CYS Chi-restraints excluded: chain I residue 144 ASP Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 178 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 9.9990 chunk 171 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 158 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15353 Z= 0.316 Angle : 0.676 14.354 20809 Z= 0.341 Chirality : 0.045 0.180 2365 Planarity : 0.004 0.052 2625 Dihedral : 5.296 53.520 2096 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 3.38 % Allowed : 21.11 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -1.24 (0.20), residues: 1830 helix: 1.40 (0.21), residues: 636 sheet: -0.80 (0.26), residues: 401 loop : -2.82 (0.20), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 100 HIS 0.015 0.001 HIS E 62 PHE 0.014 0.001 PHE A 652 TYR 0.020 0.002 TYR F 77 ARG 0.008 0.000 ARG F 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 146 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 THR cc_start: 0.8452 (OUTLIER) cc_final: 0.8247 (p) REVERT: A 642 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8912 (mt) REVERT: A 940 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8748 (tt) REVERT: B 51 ASP cc_start: 0.8680 (t0) cc_final: 0.8032 (t0) REVERT: B 223 ASN cc_start: 0.7790 (OUTLIER) cc_final: 0.6881 (t0) REVERT: B 238 HIS cc_start: 0.8345 (OUTLIER) cc_final: 0.7877 (t70) REVERT: C 31 ARG cc_start: 0.8307 (ttt-90) cc_final: 0.7652 (ptt-90) REVERT: C 236 ASP cc_start: 0.8390 (p0) cc_final: 0.7801 (t0) REVERT: D 43 TYR cc_start: 0.6644 (OUTLIER) cc_final: 0.6203 (t80) REVERT: E 91 TYR cc_start: 0.8701 (m-10) cc_final: 0.8232 (m-80) REVERT: F 106 MET cc_start: 0.8316 (mmm) cc_final: 0.7914 (mmp) REVERT: I 178 LEU cc_start: 0.4590 (OUTLIER) cc_final: 0.4185 (pp) outliers start: 55 outliers final: 43 residues processed: 188 average time/residue: 0.2821 time to fit residues: 77.9186 Evaluate side-chains 190 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 140 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 338 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 881 ARG Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 979 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain E residue 26 GLN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 75 ASN Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 147 HIS Chi-restraints excluded: chain I residue 135 CYS Chi-restraints excluded: chain I residue 144 ASP Chi-restraints excluded: chain I residue 178 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 83 optimal weight: 0.8980 chunk 122 optimal weight: 10.0000 chunk 185 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 HIS ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15353 Z= 0.314 Angle : 0.688 14.781 20809 Z= 0.346 Chirality : 0.045 0.181 2365 Planarity : 0.004 0.048 2625 Dihedral : 5.336 53.803 2096 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 3.38 % Allowed : 21.29 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -1.26 (0.20), residues: 1830 helix: 1.35 (0.21), residues: 636 sheet: -0.79 (0.26), residues: 400 loop : -2.81 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 100 HIS 0.005 0.001 HIS A 294 PHE 0.014 0.001 PHE B 176 TYR 0.021 0.002 TYR H 144 ARG 0.013 0.001 ARG H 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 140 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 THR cc_start: 0.8467 (OUTLIER) cc_final: 0.8260 (p) REVERT: A 632 MET cc_start: 0.8342 (ptp) cc_final: 0.7939 (ptp) REVERT: A 642 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8901 (mt) REVERT: A 940 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8661 (tp) REVERT: B 51 ASP cc_start: 0.8693 (t0) cc_final: 0.8054 (t0) REVERT: B 60 MET cc_start: 0.8231 (tmm) cc_final: 0.7907 (ttp) REVERT: B 223 ASN cc_start: 0.7803 (OUTLIER) cc_final: 0.6882 (t0) REVERT: B 238 HIS cc_start: 0.8411 (OUTLIER) cc_final: 0.7864 (t70) REVERT: C 31 ARG cc_start: 0.8313 (ttt-90) cc_final: 0.7661 (ptt-90) REVERT: D 43 TYR cc_start: 0.6850 (OUTLIER) cc_final: 0.6378 (t80) REVERT: E 91 TYR cc_start: 0.8709 (m-10) cc_final: 0.8249 (m-80) REVERT: F 106 MET cc_start: 0.8322 (mmm) cc_final: 0.7912 (mmp) REVERT: I 178 LEU cc_start: 0.4625 (OUTLIER) cc_final: 0.4207 (pp) outliers start: 55 outliers final: 44 residues processed: 183 average time/residue: 0.2743 time to fit residues: 73.7974 Evaluate side-chains 190 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 139 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 338 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 881 ARG Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 979 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain E residue 26 GLN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 75 ASN Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 147 HIS Chi-restraints excluded: chain I residue 135 CYS Chi-restraints excluded: chain I residue 144 ASP Chi-restraints excluded: chain I residue 178 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 147 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 151 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.095517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.069288 restraints weight = 43799.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.072904 restraints weight = 24180.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.073477 restraints weight = 14293.082| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15353 Z= 0.231 Angle : 0.654 15.132 20809 Z= 0.326 Chirality : 0.044 0.181 2365 Planarity : 0.004 0.050 2625 Dihedral : 5.188 54.493 2096 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 3.02 % Allowed : 21.91 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.20), residues: 1830 helix: 1.45 (0.21), residues: 638 sheet: -0.65 (0.26), residues: 405 loop : -2.75 (0.20), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 100 HIS 0.005 0.001 HIS A 294 PHE 0.017 0.001 PHE A 652 TYR 0.023 0.001 TYR H 144 ARG 0.013 0.000 ARG H 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2805.65 seconds wall clock time: 51 minutes 37.56 seconds (3097.56 seconds total)