Starting phenix.real_space_refine on Mon Mar 18 07:12:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6a_22074/03_2024/6x6a_22074.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6a_22074/03_2024/6x6a_22074.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/6x6a_22074/03_2024/6x6a_22074.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6a_22074/03_2024/6x6a_22074.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6a_22074/03_2024/6x6a_22074.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6a_22074/03_2024/6x6a_22074.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= 0.002 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 100 5.16 5 C 13051 2.51 5 N 3429 2.21 5 O 3660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 55": "OD1" <-> "OD2" Residue "A TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 437": "OD1" <-> "OD2" Residue "A GLU 446": "OE1" <-> "OE2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 509": "OE1" <-> "OE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 537": "OE1" <-> "OE2" Residue "A PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 581": "OD1" <-> "OD2" Residue "A PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 707": "OE1" <-> "OE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 796": "OE1" <-> "OE2" Residue "A TYR 830": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 861": "OE1" <-> "OE2" Residue "B TYR 1098": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 1265": "OD1" <-> "OD2" Residue "G GLU 1267": "OE1" <-> "OE2" Residue "G ARG 1274": "NH1" <-> "NH2" Residue "G GLU 1306": "OE1" <-> "OE2" Residue "G GLU 1308": "OE1" <-> "OE2" Residue "G ASP 1317": "OD1" <-> "OD2" Residue "G PHE 1323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 1324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1347": "OE1" <-> "OE2" Residue "C ARG 1227": "NH1" <-> "NH2" Residue "C PHE 1248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 63": "OD1" <-> "OD2" Residue "D TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "D GLU 98": "OE1" <-> "OE2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "D GLU 130": "OE1" <-> "OE2" Residue "D ARG 133": "NH1" <-> "NH2" Residue "D PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 251": "OD1" <-> "OD2" Residue "D TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 284": "OE1" <-> "OE2" Residue "D PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 394": "OE1" <-> "OE2" Residue "D GLU 415": "OE1" <-> "OE2" Residue "D TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 446": "OE1" <-> "OE2" Residue "D PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 486": "OE1" <-> "OE2" Residue "D GLU 509": "OE1" <-> "OE2" Residue "D PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 581": "OD1" <-> "OD2" Residue "D GLU 609": "OE1" <-> "OE2" Residue "D PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 707": "OE1" <-> "OE2" Residue "D PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 782": "OE1" <-> "OE2" Residue "D GLU 796": "OE1" <-> "OE2" Residue "D GLU 809": "OE1" <-> "OE2" Residue "D TYR 830": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1153": "OD1" <-> "OD2" Residue "E PHE 1187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 1256": "OD1" <-> "OD2" Residue "I PHE 1270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 1306": "OE1" <-> "OE2" Residue "F ARG 1227": "NH1" <-> "NH2" Residue "F GLU 1244": "OE1" <-> "OE2" Residue "F PHE 1248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 1264": "OD1" <-> "OD2" Residue "F GLU 1306": "OE1" <-> "OE2" Residue "F GLU 1308": "OE1" <-> "OE2" Residue "F TYR 1324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 1338": "OD1" <-> "OD2" Residue "F GLU 1347": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20240 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 846, 6816 Classifications: {'peptide': 846} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 54, 'TRANS': 791} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1068 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 10, 'TRANS': 123} Chain: "G" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1107 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1136 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 132} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 6816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 846, 6816 Classifications: {'peptide': 846} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 54, 'TRANS': 791} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1053 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 123} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "I" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1103 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 127} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1141 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 132} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.41, per 1000 atoms: 0.51 Number of scatterers: 20240 At special positions: 0 Unit cell: (129.525, 161.7, 114.675, 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 100 16.00 O 3660 8.00 N 3429 7.00 C 13051 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.25 Conformation dependent library (CDL) restraints added in 3.6 seconds 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4696 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 39 sheets defined 18.7% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing helix chain 'A' and resid 30 through 49 removed outlier: 4.191A pdb=" N TYR A 44 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LEU A 47 " --> pdb=" O LYS A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.540A pdb=" N VAL A 120 " --> pdb=" O HIS A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 341 through 346 Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 392 through 403 Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 583 through 587 Processing helix chain 'A' and resid 661 through 671 removed outlier: 3.608A pdb=" N ASN A 665 " --> pdb=" O TYR A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 691 Processing helix chain 'A' and resid 692 through 694 No H-bonds generated for 'chain 'A' and resid 692 through 694' Processing helix chain 'A' and resid 700 through 716 Processing helix chain 'A' and resid 730 through 743 Processing helix chain 'A' and resid 758 through 762 Processing helix chain 'A' and resid 763 through 771 removed outlier: 4.295A pdb=" N ARG A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 785 Processing helix chain 'A' and resid 786 through 793 removed outlier: 3.825A pdb=" N VAL A 790 " --> pdb=" O ALA A 787 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N GLU A 791 " --> pdb=" O LEU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 827 removed outlier: 4.297A pdb=" N THR A 816 " --> pdb=" O HIS A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 863 Processing helix chain 'B' and resid 1132 through 1137 removed outlier: 3.565A pdb=" N GLY B1137 " --> pdb=" O ASP B1133 " (cutoff:3.500A) Processing helix chain 'G' and resid 1256 through 1270 Processing helix chain 'C' and resid 1258 through 1270 removed outlier: 4.133A pdb=" N ALA C1262 " --> pdb=" O SER C1258 " (cutoff:3.500A) Processing helix chain 'C' and resid 1295 through 1300 removed outlier: 4.120A pdb=" N MET C1299 " --> pdb=" O SER C1295 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 49 removed outlier: 3.801A pdb=" N TYR D 44 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 120 removed outlier: 3.544A pdb=" N VAL D 120 " --> pdb=" O HIS D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 133 Processing helix chain 'D' and resid 243 through 250 Processing helix chain 'D' and resid 294 through 298 Processing helix chain 'D' and resid 341 through 346 Processing helix chain 'D' and resid 382 through 384 No H-bonds generated for 'chain 'D' and resid 382 through 384' Processing helix chain 'D' and resid 392 through 403 Processing helix chain 'D' and resid 661 through 671 removed outlier: 3.622A pdb=" N ASN D 665 " --> pdb=" O TYR D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 691 Processing helix chain 'D' and resid 692 through 694 No H-bonds generated for 'chain 'D' and resid 692 through 694' Processing helix chain 'D' and resid 700 through 716 Processing helix chain 'D' and resid 730 through 743 Processing helix chain 'D' and resid 758 through 762 Processing helix chain 'D' and resid 763 through 771 removed outlier: 4.095A pdb=" N ARG D 769 " --> pdb=" O GLY D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 777 through 785 Processing helix chain 'D' and resid 786 through 793 removed outlier: 4.033A pdb=" N VAL D 790 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLU D 791 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 812 through 827 removed outlier: 4.393A pdb=" N THR D 816 " --> pdb=" O HIS D 812 " (cutoff:3.500A) Processing helix chain 'D' and resid 844 through 863 Processing helix chain 'E' and resid 1132 through 1137 Processing helix chain 'E' and resid 1141 through 1145 Processing helix chain 'I' and resid 1256 through 1270 Processing helix chain 'F' and resid 1228 through 1236 removed outlier: 3.788A pdb=" N SER F1233 " --> pdb=" O ILE F1229 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL F1234 " --> pdb=" O PRO F1230 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU F1236 " --> pdb=" O THR F1232 " (cutoff:3.500A) Processing helix chain 'F' and resid 1258 through 1270 Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 60 removed outlier: 5.954A pdb=" N ASP A 55 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU A 75 " --> pdb=" O ASP A 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 103 removed outlier: 3.652A pdb=" N LEU A 100 " --> pdb=" O LEU B1194 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL G1217 " --> pdb=" O ALA B1185 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE B1187 " --> pdb=" O LEU G1215 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LEU G1215 " --> pdb=" O PHE B1187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 145 removed outlier: 4.135A pdb=" N ALA A 155 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A 158 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 189 through 193 removed outlier: 6.491A pdb=" N SER A 202 " --> pdb=" O PRO A 191 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ILE A 193 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N PHE A 200 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 237 through 239 removed outlier: 3.679A pdb=" N SER A 263 " --> pdb=" O THR A 272 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 256 through 258 removed outlier: 9.093A pdb=" N LEU A 317 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU A 338 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 287 through 291 Processing sheet with id=AA8, first strand: chain 'A' and resid 351 through 357 removed outlier: 5.470A pdb=" N ILE A 352 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU A 369 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 354 " --> pdb=" O MET A 367 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU A 376 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU A 414 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU A 378 " --> pdb=" O VAL A 412 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 427 through 429 removed outlier: 3.527A pdb=" N HIS A 453 " --> pdb=" O ASN A 445 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 505 through 507 Processing sheet with id=AB2, first strand: chain 'A' and resid 547 through 552 removed outlier: 6.458A pdb=" N VAL A 572 " --> pdb=" O MET A 595 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LYS A 576 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N PHE A 591 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER A 578 " --> pdb=" O PRO A 589 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 609 through 614 removed outlier: 4.457A pdb=" N ILE A 677 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 10.207A pdb=" N HIS A 637 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ARG A 723 " --> pdb=" O HIS A 637 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N TRP A 729 " --> pdb=" O VAL A 643 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ALA A 750 " --> pdb=" O LEU A 801 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU A 803 " --> pdb=" O ALA A 750 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA A 752 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLY A 805 " --> pdb=" O ALA A 752 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1089 through 1092 removed outlier: 3.671A pdb=" N VAL B1091 " --> pdb=" O LEU B1097 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N LEU B1097 " --> pdb=" O VAL B1091 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B1123 " --> pdb=" O PHE B1102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1116 through 1118 removed outlier: 3.837A pdb=" N VAL B1164 " --> pdb=" O LEU B1207 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B1199 " --> pdb=" O VAL B1206 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 1230 through 1231 removed outlier: 3.550A pdb=" N LEU G1284 " --> pdb=" O VAL G1231 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 1238 through 1239 removed outlier: 3.531A pdb=" N VAL G1273 " --> pdb=" O HIS G1239 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 1247 through 1251 removed outlier: 3.512A pdb=" N TYR G1324 " --> pdb=" O GLU G1301 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU G1301 " --> pdb=" O TYR G1324 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 1306 through 1308 removed outlier: 4.176A pdb=" N VAL G1336 " --> pdb=" O TRP G1346 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N TRP G1346 " --> pdb=" O VAL G1336 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASP G1338 " --> pdb=" O LEU G1344 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU G1344 " --> pdb=" O ASP G1338 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 1238 through 1241 removed outlier: 6.069A pdb=" N VAL C1246 " --> pdb=" O VAL C1325 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 1306 through 1309 removed outlier: 3.851A pdb=" N LEU C1309 " --> pdb=" O CYS C1288 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N CYS C1288 " --> pdb=" O LEU C1309 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE C1332 " --> pdb=" O VAL C1350 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 54 through 60 removed outlier: 4.291A pdb=" N PHE D 56 " --> pdb=" O TYR D 73 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TYR D 73 " --> pdb=" O PHE D 56 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N PHE D 58 " --> pdb=" O ARG D 71 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG D 71 " --> pdb=" O PHE D 58 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N GLN D 60 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N SER D 69 " --> pdb=" O GLN D 60 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 100 through 103 removed outlier: 3.686A pdb=" N LEU D 100 " --> pdb=" O LEU E1194 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 142 through 145 Processing sheet with id=AC6, first strand: chain 'D' and resid 189 through 193 removed outlier: 6.463A pdb=" N SER D 202 " --> pdb=" O PRO D 191 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ILE D 193 " --> pdb=" O PHE D 200 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N PHE D 200 " --> pdb=" O ILE D 193 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 237 through 239 Processing sheet with id=AC8, first strand: chain 'D' and resid 256 through 258 removed outlier: 9.030A pdb=" N LEU D 317 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU D 338 " --> pdb=" O LEU D 317 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 287 through 291 Processing sheet with id=AD1, first strand: chain 'D' and resid 351 through 357 removed outlier: 6.686A pdb=" N MET D 367 " --> pdb=" O ALA D 353 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ALA D 355 " --> pdb=" O TRP D 365 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TRP D 365 " --> pdb=" O ALA D 355 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU D 376 " --> pdb=" O GLU D 414 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU D 414 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU D 378 " --> pdb=" O VAL D 412 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 427 through 429 Processing sheet with id=AD3, first strand: chain 'D' and resid 505 through 507 Processing sheet with id=AD4, first strand: chain 'D' and resid 547 through 552 removed outlier: 6.586A pdb=" N VAL D 572 " --> pdb=" O MET D 595 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LYS D 576 " --> pdb=" O PHE D 591 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N PHE D 591 " --> pdb=" O LYS D 576 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER D 578 " --> pdb=" O PRO D 589 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 609 through 614 removed outlier: 4.309A pdb=" N TYR D 622 " --> pdb=" O ASP D 678 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE D 677 " --> pdb=" O PHE D 642 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N HIS D 637 " --> pdb=" O LEU D 721 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ARG D 723 " --> pdb=" O HIS D 637 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL D 749 " --> pdb=" O SER D 722 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL D 724 " --> pdb=" O VAL D 749 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ILE D 751 " --> pdb=" O VAL D 724 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE D 726 " --> pdb=" O ILE D 751 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLY D 753 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLY D 728 " --> pdb=" O GLY D 753 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA D 750 " --> pdb=" O LEU D 801 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N LEU D 803 " --> pdb=" O ALA D 750 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA D 752 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N GLY D 805 " --> pdb=" O ALA D 752 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 1116 through 1118 removed outlier: 3.646A pdb=" N CYS E1116 " --> pdb=" O HIS E1165 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 1199 through 1200 removed outlier: 3.934A pdb=" N ARG E1199 " --> pdb=" O VAL E1206 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 1230 through 1231 removed outlier: 3.773A pdb=" N LEU I1284 " --> pdb=" O VAL I1231 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 1237 through 1238 Processing sheet with id=AE1, first strand: chain 'I' and resid 1290 through 1294 removed outlier: 7.476A pdb=" N VAL I1336 " --> pdb=" O VAL I1345 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 1273 through 1274 removed outlier: 3.997A pdb=" N THR F1247 " --> pdb=" O ARG F1240 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N VAL F1246 " --> pdb=" O VAL F1325 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 1290 through 1293 removed outlier: 6.616A pdb=" N ASP F1338 " --> pdb=" O LEU F1344 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU F1344 " --> pdb=" O ASP F1338 " (cutoff:3.500A) 676 hydrogen bonds defined for protein. 1779 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: 8.47 Time building geometry restraints manager: 7.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3347 1.32 - 1.44: 5827 1.44 - 1.57: 11501 1.57 - 1.69: 7 1.69 - 1.81: 156 Bond restraints: 20838 Sorted by residual: bond pdb=" C TYR A 731 " pdb=" O TYR A 731 " ideal model delta sigma weight residual 1.237 1.192 0.045 1.17e-02 7.31e+03 1.48e+01 bond pdb=" C GLY A 728 " pdb=" O GLY A 728 " ideal model delta sigma weight residual 1.233 1.196 0.037 9.80e-03 1.04e+04 1.40e+01 bond pdb=" C ARG A 371 " pdb=" O ARG A 371 " ideal model delta sigma weight residual 1.244 1.211 0.033 9.80e-03 1.04e+04 1.11e+01 bond pdb=" N ASN E1140 " pdb=" CA ASN E1140 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 9.60e+00 bond pdb=" C SER A 730 " pdb=" O SER A 730 " ideal model delta sigma weight residual 1.235 1.197 0.039 1.26e-02 6.30e+03 9.48e+00 ... (remaining 20833 not shown) Histogram of bond angle deviations from ideal: 95.81 - 103.50: 372 103.50 - 111.20: 7808 111.20 - 118.89: 8695 118.89 - 126.59: 11000 126.59 - 134.28: 423 Bond angle restraints: 28298 Sorted by residual: angle pdb=" N ASN E1140 " pdb=" CA ASN E1140 " pdb=" C ASN E1140 " ideal model delta sigma weight residual 112.75 124.46 -11.71 1.36e+00 5.41e-01 7.42e+01 angle pdb=" N LYS I1220 " pdb=" CA LYS I1220 " pdb=" C LYS I1220 " ideal model delta sigma weight residual 111.28 120.22 -8.94 1.09e+00 8.42e-01 6.73e+01 angle pdb=" N TRP D 729 " pdb=" CA TRP D 729 " pdb=" C TRP D 729 " ideal model delta sigma weight residual 111.96 123.41 -11.45 1.41e+00 5.03e-01 6.59e+01 angle pdb=" CA TRP D 729 " pdb=" C TRP D 729 " pdb=" N SER D 730 " ideal model delta sigma weight residual 117.34 126.21 -8.87 1.22e+00 6.72e-01 5.28e+01 angle pdb=" N ILE I1302 " pdb=" CA ILE I1302 " pdb=" C ILE I1302 " ideal model delta sigma weight residual 107.75 117.75 -10.00 1.42e+00 4.96e-01 4.96e+01 ... (remaining 28293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 11053 17.76 - 35.52: 1061 35.52 - 53.28: 169 53.28 - 71.03: 47 71.03 - 88.79: 12 Dihedral angle restraints: 12342 sinusoidal: 5024 harmonic: 7318 Sorted by residual: dihedral pdb=" CA TYR D 770 " pdb=" C TYR D 770 " pdb=" N MET D 771 " pdb=" CA MET D 771 " ideal model delta harmonic sigma weight residual 180.00 150.54 29.46 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA LEU C1300 " pdb=" C LEU C1300 " pdb=" N GLU C1301 " pdb=" CA GLU C1301 " ideal model delta harmonic sigma weight residual -180.00 -151.67 -28.33 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA SER I1233 " pdb=" C SER I1233 " pdb=" N VAL I1234 " pdb=" CA VAL I1234 " ideal model delta harmonic sigma weight residual -180.00 -152.73 -27.27 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 12339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2410 0.093 - 0.185: 506 0.185 - 0.278: 77 0.278 - 0.370: 16 0.370 - 0.463: 4 Chirality restraints: 3013 Sorted by residual: chirality pdb=" CB ILE C1302 " pdb=" CA ILE C1302 " pdb=" CG1 ILE C1302 " pdb=" CG2 ILE C1302 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.35e+00 chirality pdb=" CA ASN E1140 " pdb=" N ASN E1140 " pdb=" C ASN E1140 " pdb=" CB ASN E1140 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" CB ILE D 426 " pdb=" CA ILE D 426 " pdb=" CG1 ILE D 426 " pdb=" CG2 ILE D 426 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.96e+00 ... (remaining 3010 not shown) Planarity restraints: 3657 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL I1292 " 0.020 2.00e-02 2.50e+03 4.06e-02 1.64e+01 pdb=" C VAL I1292 " -0.070 2.00e-02 2.50e+03 pdb=" O VAL I1292 " 0.026 2.00e-02 2.50e+03 pdb=" N SER I1293 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 393 " 0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C GLU A 393 " -0.065 2.00e-02 2.50e+03 pdb=" O GLU A 393 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU A 394 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 393 " -0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C GLU D 393 " 0.062 2.00e-02 2.50e+03 pdb=" O GLU D 393 " -0.023 2.00e-02 2.50e+03 pdb=" N GLU D 394 " -0.021 2.00e-02 2.50e+03 ... (remaining 3654 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 2520 2.74 - 3.28: 19071 3.28 - 3.82: 35094 3.82 - 4.36: 41632 4.36 - 4.90: 71084 Nonbonded interactions: 169401 Sorted by model distance: nonbonded pdb=" OH TYR A 644 " pdb=" O SER C1213 " model vdw 2.206 2.440 nonbonded pdb=" OH TYR D 73 " pdb=" OD2 ASP D 164 " model vdw 2.210 2.440 nonbonded pdb=" CG TYR G1238 " pdb=" OE2 GLU G1267 " model vdw 2.213 3.260 nonbonded pdb=" O LYS A 348 " pdb=" OD1 ASP A 370 " model vdw 2.225 3.040 nonbonded pdb=" OG SER D 230 " pdb=" OD1 ASN D 231 " model vdw 2.254 2.440 ... (remaining 169396 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = (chain 'B' and ((resid 1079 through 1080 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1081 through 1212)) selection = chain 'E' } ncs_group { reference = (chain 'C' and ((resid 1213 and (name CA or name C or name O or name CB or name \ OG )) or resid 1214 through 1276 or (resid 1277 and (name N or name CA or name C \ or name O or name CB )) or resid 1278 through 1350)) selection = (chain 'F' and ((resid 1213 and (name CA or name C or name O or name CB or name \ OG )) or resid 1214 through 1225 or (resid 1226 and (name N or name CA or name C \ or name O or name CB )) or resid 1227 or (resid 1228 through 1229 and (name N o \ r name CA or name C or name O or name CB )) or resid 1230 through 1350)) selection = (chain 'G' and (resid 1213 through 1219 or (resid 1220 and (name N or name CA or \ name C or name O or name CB )) or resid 1221 through 1225 or (resid 1226 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1227 or (resid 1228 \ through 1229 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 230 through 1276 or (resid 1277 and (name N or name CA or name C or name O or na \ me CB )) or resid 1278 through 1350)) selection = (chain 'I' and (resid 1213 through 1219 or (resid 1220 and (name N or name CA or \ name C or name O or name CB )) or resid 1221 through 1225 or (resid 1226 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1227 or (resid 1228 \ through 1229 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 230 through 1350)) } 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=0.45 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: 4.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.770 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 55.610 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 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 : 0.010 0.112 20838 Z= 0.666 Angle : 1.291 13.382 28298 Z= 0.727 Chirality : 0.078 0.463 3013 Planarity : 0.009 0.085 3657 Dihedral : 14.434 88.793 7646 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.50 % Favored : 92.38 % Rotamer: Outliers : 0.45 % Allowed : 1.27 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.80 (0.15), residues: 2508 helix: -1.59 (0.23), residues: 378 sheet: -2.25 (0.17), residues: 724 loop : -1.66 (0.15), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP A 375 HIS 0.024 0.003 HIS A 111 PHE 0.056 0.004 PHE D 711 TYR 0.056 0.004 TYR A 781 ARG 0.020 0.001 ARG G1333 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 267 time to evaluate : 2.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.8060 (t0) cc_final: 0.7526 (t70) REVERT: A 738 MET cc_start: 0.8501 (mmm) cc_final: 0.8223 (mmm) REVERT: B 1099 ARG cc_start: 0.7178 (mtp-110) cc_final: 0.6868 (mtp180) REVERT: B 1119 MET cc_start: 0.6018 (ptp) cc_final: 0.5776 (pmm) REVERT: B 1178 ASP cc_start: 0.7384 (t0) cc_final: 0.7111 (t70) REVERT: B 1203 HIS cc_start: 0.6519 (m-70) cc_final: 0.6314 (m170) REVERT: G 1263 ILE cc_start: 0.7810 (pt) cc_final: 0.7471 (pt) REVERT: G 1330 SER cc_start: 0.7451 (t) cc_final: 0.7018 (m) REVERT: C 1260 ARG cc_start: 0.7587 (mtp180) cc_final: 0.7124 (ttt-90) REVERT: C 1286 MET cc_start: 0.3543 (ptt) cc_final: 0.3216 (ptm) REVERT: D 251 ASP cc_start: 0.8025 (m-30) cc_final: 0.7723 (t0) REVERT: D 684 GLN cc_start: 0.7870 (mp10) cc_final: 0.7034 (mp10) REVERT: E 1096 ASN cc_start: 0.7374 (t0) cc_final: 0.7122 (t0) REVERT: E 1119 MET cc_start: 0.5535 (tpp) cc_final: 0.5066 (mpp) REVERT: I 1227 ARG cc_start: 0.6008 (tpp-160) cc_final: 0.5740 (tpp-160) REVERT: I 1338 ASP cc_start: 0.6554 (t0) cc_final: 0.6299 (t0) REVERT: F 1289 ARG cc_start: 0.7427 (mtt180) cc_final: 0.7157 (mtm-85) outliers start: 10 outliers final: 5 residues processed: 276 average time/residue: 0.3730 time to fit residues: 153.2654 Evaluate side-chains 208 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 203 time to evaluate : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 1217 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain I residue 1320 PHE Chi-restraints excluded: chain I residue 1332 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 10.0000 chunk 187 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 194 optimal weight: 0.0770 chunk 75 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 225 optimal weight: 4.9990 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 GLN A 810 ASN ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1204 HIS ** G1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1335 GLN E1140 ASN E1165 HIS I1335 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20838 Z= 0.226 Angle : 0.672 10.271 28298 Z= 0.351 Chirality : 0.047 0.196 3013 Planarity : 0.006 0.065 3657 Dihedral : 6.311 38.450 2751 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.91 % Allowed : 8.11 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.10 (0.16), residues: 2508 helix: -0.44 (0.25), residues: 393 sheet: -1.81 (0.17), residues: 764 loop : -1.36 (0.16), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 375 HIS 0.006 0.001 HIS D 54 PHE 0.018 0.001 PHE I1228 TYR 0.017 0.002 TYR C1290 ARG 0.007 0.000 ARG A 769 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 229 time to evaluate : 2.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.8134 (t0) cc_final: 0.7648 (t70) REVERT: A 738 MET cc_start: 0.8430 (mmm) cc_final: 0.8228 (mmm) REVERT: B 1119 MET cc_start: 0.6293 (ptp) cc_final: 0.5946 (pmm) REVERT: B 1187 PHE cc_start: 0.7890 (m-80) cc_final: 0.7636 (m-10) REVERT: B 1194 LEU cc_start: 0.8287 (mt) cc_final: 0.7860 (mt) REVERT: G 1260 ARG cc_start: 0.7204 (mtm180) cc_final: 0.6894 (mtm180) REVERT: G 1330 SER cc_start: 0.7484 (t) cc_final: 0.7098 (m) REVERT: C 1260 ARG cc_start: 0.7662 (mtp180) cc_final: 0.7267 (ttt-90) REVERT: C 1323 PHE cc_start: 0.5075 (t80) cc_final: 0.4756 (t80) REVERT: D 251 ASP cc_start: 0.8086 (m-30) cc_final: 0.7692 (t0) REVERT: D 684 GLN cc_start: 0.7669 (mp10) cc_final: 0.7060 (mp10) REVERT: D 738 MET cc_start: 0.8579 (mmm) cc_final: 0.8313 (mmm) REVERT: E 1096 ASN cc_start: 0.7487 (t0) cc_final: 0.6955 (t0) REVERT: E 1119 MET cc_start: 0.5422 (tpp) cc_final: 0.4760 (mtm) REVERT: I 1338 ASP cc_start: 0.6394 (t0) cc_final: 0.6121 (t0) REVERT: F 1289 ARG cc_start: 0.7367 (mtt180) cc_final: 0.7082 (mtm-85) REVERT: F 1335 GLN cc_start: 0.6968 (mp10) cc_final: 0.6280 (mp10) outliers start: 20 outliers final: 15 residues processed: 239 average time/residue: 0.3625 time to fit residues: 130.2623 Evaluate side-chains 221 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 206 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain G residue 1299 MET Chi-restraints excluded: chain G residue 1338 ASP Chi-restraints excluded: chain D residue 39 HIS Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 433 SER Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain E residue 1112 ASN Chi-restraints excluded: chain E residue 1125 VAL Chi-restraints excluded: chain I residue 1320 PHE Chi-restraints excluded: chain I residue 1332 ILE Chi-restraints excluded: chain F residue 1217 VAL Chi-restraints excluded: chain F residue 1218 LEU Chi-restraints excluded: chain F residue 1239 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 187 optimal weight: 3.9990 chunk 153 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 225 optimal weight: 3.9990 chunk 243 optimal weight: 0.4980 chunk 200 optimal weight: 0.7980 chunk 223 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 180 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 810 ASN ** B1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1335 GLN ** C1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 516 GLN D 837 ASN ** I1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20838 Z= 0.202 Angle : 0.611 10.312 28298 Z= 0.316 Chirality : 0.045 0.175 3013 Planarity : 0.005 0.056 3657 Dihedral : 5.756 35.608 2746 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.27 % Allowed : 11.88 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.65 (0.16), residues: 2508 helix: 0.02 (0.27), residues: 395 sheet: -1.42 (0.18), residues: 741 loop : -1.19 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 375 HIS 0.006 0.001 HIS A 111 PHE 0.024 0.001 PHE G1272 TYR 0.015 0.001 TYR F1311 ARG 0.005 0.000 ARG F1260 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 231 time to evaluate : 2.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.8119 (t0) cc_final: 0.7629 (t70) REVERT: B 1129 PHE cc_start: 0.7528 (m-80) cc_final: 0.6979 (m-80) REVERT: G 1260 ARG cc_start: 0.7188 (mtm180) cc_final: 0.6900 (mtm180) REVERT: C 1260 ARG cc_start: 0.7595 (mtp180) cc_final: 0.7281 (ttt-90) REVERT: C 1268 MET cc_start: 0.4282 (mmm) cc_final: 0.3919 (mtt) REVERT: D 251 ASP cc_start: 0.8033 (m-30) cc_final: 0.7603 (t0) REVERT: E 1096 ASN cc_start: 0.7367 (t0) cc_final: 0.6862 (t0) REVERT: I 1338 ASP cc_start: 0.6435 (t0) cc_final: 0.6129 (t0) REVERT: F 1236 LEU cc_start: 0.7899 (mt) cc_final: 0.7533 (tp) REVERT: F 1260 ARG cc_start: 0.7520 (ttt-90) cc_final: 0.6840 (ptm160) REVERT: F 1289 ARG cc_start: 0.7274 (mtt180) cc_final: 0.7044 (mtm-85) REVERT: F 1320 PHE cc_start: 0.5468 (p90) cc_final: 0.5084 (p90) outliers start: 28 outliers final: 13 residues processed: 246 average time/residue: 0.3728 time to fit residues: 135.9990 Evaluate side-chains 215 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 202 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain G residue 1338 ASP Chi-restraints excluded: chain D residue 39 HIS Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 772 ASP Chi-restraints excluded: chain E residue 1125 VAL Chi-restraints excluded: chain I residue 1320 PHE Chi-restraints excluded: chain F residue 1218 LEU Chi-restraints excluded: chain F residue 1221 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 10.0000 chunk 169 optimal weight: 6.9990 chunk 117 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 chunk 226 optimal weight: 5.9990 chunk 239 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 214 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS A 445 ASN A 810 ASN ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1335 GLN D 374 GLN D 632 GLN D 798 ASN ** I1335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 20838 Z= 0.550 Angle : 0.751 10.367 28298 Z= 0.388 Chirality : 0.049 0.242 3013 Planarity : 0.006 0.104 3657 Dihedral : 5.917 27.919 2742 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.26 % Allowed : 13.92 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.73 (0.16), residues: 2508 helix: 0.21 (0.27), residues: 368 sheet: -1.55 (0.18), residues: 739 loop : -1.25 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 375 HIS 0.010 0.002 HIS D 804 PHE 0.018 0.002 PHE A 151 TYR 0.021 0.002 TYR D 835 ARG 0.021 0.001 ARG I1333 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 205 time to evaluate : 2.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1129 PHE cc_start: 0.7526 (m-80) cc_final: 0.7222 (m-80) REVERT: B 1151 LEU cc_start: 0.8365 (tp) cc_final: 0.8163 (tp) REVERT: G 1260 ARG cc_start: 0.7483 (mtm180) cc_final: 0.7274 (mtm180) REVERT: G 1323 PHE cc_start: 0.7099 (t80) cc_final: 0.6788 (t80) REVERT: G 1330 SER cc_start: 0.7570 (t) cc_final: 0.7174 (m) REVERT: C 1260 ARG cc_start: 0.7598 (mtp180) cc_final: 0.7324 (ttt-90) REVERT: D 251 ASP cc_start: 0.8181 (m-30) cc_final: 0.7732 (t0) REVERT: E 1096 ASN cc_start: 0.7277 (t0) cc_final: 0.6837 (t0) REVERT: I 1215 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8616 (tt) REVERT: I 1261 LYS cc_start: 0.7597 (tppt) cc_final: 0.7301 (tptt) REVERT: I 1305 LYS cc_start: 0.7220 (mttt) cc_final: 0.6772 (ttmm) REVERT: I 1338 ASP cc_start: 0.6636 (t0) cc_final: 0.6306 (t0) REVERT: F 1274 ARG cc_start: 0.2749 (OUTLIER) cc_final: 0.2363 (mtt90) REVERT: F 1289 ARG cc_start: 0.7427 (mtt180) cc_final: 0.7220 (mtm-85) outliers start: 72 outliers final: 39 residues processed: 260 average time/residue: 0.3599 time to fit residues: 140.3141 Evaluate side-chains 229 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 188 time to evaluate : 2.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain B residue 1140 ASN Chi-restraints excluded: chain B residue 1192 MET Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1203 HIS Chi-restraints excluded: chain G residue 1292 VAL Chi-restraints excluded: chain G residue 1338 ASP Chi-restraints excluded: chain G residue 1350 VAL Chi-restraints excluded: chain C residue 1218 LEU Chi-restraints excluded: chain D residue 39 HIS Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 625 ILE Chi-restraints excluded: chain D residue 709 LEU Chi-restraints excluded: chain D residue 729 TRP Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 771 MET Chi-restraints excluded: chain D residue 772 ASP Chi-restraints excluded: chain E residue 1112 ASN Chi-restraints excluded: chain E residue 1125 VAL Chi-restraints excluded: chain E residue 1154 ILE Chi-restraints excluded: chain E residue 1200 VAL Chi-restraints excluded: chain I residue 1215 LEU Chi-restraints excluded: chain I residue 1241 VAL Chi-restraints excluded: chain I residue 1332 ILE Chi-restraints excluded: chain F residue 1217 VAL Chi-restraints excluded: chain F residue 1218 LEU Chi-restraints excluded: chain F residue 1221 MET Chi-restraints excluded: chain F residue 1239 HIS Chi-restraints excluded: chain F residue 1241 VAL Chi-restraints excluded: chain F residue 1274 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 178 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 204 optimal weight: 0.5980 chunk 165 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 215 optimal weight: 0.3980 chunk 60 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 HIS A 810 ASN ** G1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1335 GLN ** C1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 742 HIS ** I1335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20838 Z= 0.204 Angle : 0.619 9.565 28298 Z= 0.318 Chirality : 0.045 0.320 3013 Planarity : 0.005 0.068 3657 Dihedral : 5.488 24.813 2740 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.45 % Allowed : 15.50 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.45 (0.17), residues: 2508 helix: 0.53 (0.28), residues: 375 sheet: -1.35 (0.18), residues: 749 loop : -1.10 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 375 HIS 0.014 0.001 HIS D 742 PHE 0.024 0.001 PHE B1182 TYR 0.016 0.001 TYR A 835 ARG 0.007 0.000 ARG I1333 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 215 time to evaluate : 2.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.8117 (t0) cc_final: 0.7565 (t70) REVERT: A 771 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.6946 (mtt) REVERT: B 1129 PHE cc_start: 0.7463 (m-80) cc_final: 0.7122 (m-80) REVERT: B 1184 MET cc_start: 0.7592 (ppp) cc_final: 0.7040 (tmm) REVERT: G 1227 ARG cc_start: 0.7785 (mmm160) cc_final: 0.7412 (mmp-170) REVERT: G 1228 PHE cc_start: 0.5658 (m-80) cc_final: 0.5217 (m-80) REVERT: G 1260 ARG cc_start: 0.7394 (mtm180) cc_final: 0.7190 (mtm180) REVERT: G 1323 PHE cc_start: 0.6931 (t80) cc_final: 0.6574 (t80) REVERT: G 1330 SER cc_start: 0.7551 (t) cc_final: 0.7167 (m) REVERT: C 1260 ARG cc_start: 0.7604 (mtp180) cc_final: 0.7342 (ttt-90) REVERT: C 1268 MET cc_start: 0.3925 (mmm) cc_final: 0.3431 (mtt) REVERT: C 1272 PHE cc_start: 0.4655 (m-80) cc_final: 0.3988 (m-80) REVERT: C 1299 MET cc_start: 0.4359 (tpt) cc_final: 0.4118 (tpt) REVERT: D 251 ASP cc_start: 0.8084 (m-30) cc_final: 0.7610 (t0) REVERT: D 632 GLN cc_start: 0.8490 (tp-100) cc_final: 0.8279 (tp-100) REVERT: D 710 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7797 (mp10) REVERT: D 771 MET cc_start: 0.7732 (mtt) cc_final: 0.7429 (mtt) REVERT: E 1096 ASN cc_start: 0.7123 (t0) cc_final: 0.6679 (t0) REVERT: I 1215 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8577 (tt) REVERT: I 1338 ASP cc_start: 0.6612 (t0) cc_final: 0.6140 (t0) REVERT: F 1260 ARG cc_start: 0.7528 (ttt-90) cc_final: 0.6886 (ptm160) REVERT: F 1274 ARG cc_start: 0.2837 (OUTLIER) cc_final: 0.2465 (mtt90) REVERT: F 1289 ARG cc_start: 0.7328 (mtt180) cc_final: 0.7097 (mtm-85) outliers start: 54 outliers final: 33 residues processed: 254 average time/residue: 0.3662 time to fit residues: 140.1678 Evaluate side-chains 231 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 194 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain B residue 1140 ASN Chi-restraints excluded: chain B residue 1192 MET Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1205 ILE Chi-restraints excluded: chain G residue 1292 VAL Chi-restraints excluded: chain C residue 1218 LEU Chi-restraints excluded: chain C residue 1332 ILE Chi-restraints excluded: chain D residue 39 HIS Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 433 SER Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain D residue 558 MET Chi-restraints excluded: chain D residue 625 ILE Chi-restraints excluded: chain D residue 710 GLN Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 772 ASP Chi-restraints excluded: chain D residue 786 VAL Chi-restraints excluded: chain E residue 1100 VAL Chi-restraints excluded: chain E residue 1112 ASN Chi-restraints excluded: chain E residue 1154 ILE Chi-restraints excluded: chain I residue 1215 LEU Chi-restraints excluded: chain I residue 1241 VAL Chi-restraints excluded: chain F residue 1221 MET Chi-restraints excluded: chain F residue 1239 HIS Chi-restraints excluded: chain F residue 1241 VAL Chi-restraints excluded: chain F residue 1274 ARG Chi-restraints excluded: chain F residue 1325 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 0.5980 chunk 215 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS A 810 ASN ** G1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1335 GLN ** C1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 742 HIS ** I1335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20838 Z= 0.237 Angle : 0.610 8.966 28298 Z= 0.310 Chirality : 0.045 0.216 3013 Planarity : 0.005 0.055 3657 Dihedral : 5.267 23.950 2740 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.72 % Allowed : 15.50 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.33 (0.17), residues: 2508 helix: 0.73 (0.28), residues: 372 sheet: -1.22 (0.18), residues: 735 loop : -1.09 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 375 HIS 0.005 0.001 HIS A 840 PHE 0.032 0.002 PHE E1182 TYR 0.019 0.001 TYR F1251 ARG 0.005 0.000 ARG E1099 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 208 time to evaluate : 2.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.8133 (t0) cc_final: 0.7569 (t70) REVERT: B 1129 PHE cc_start: 0.7433 (m-80) cc_final: 0.7064 (m-80) REVERT: G 1227 ARG cc_start: 0.7766 (mmm160) cc_final: 0.7433 (mmp-170) REVERT: G 1228 PHE cc_start: 0.5641 (m-80) cc_final: 0.5209 (m-80) REVERT: G 1260 ARG cc_start: 0.7429 (mtm180) cc_final: 0.7214 (mtm180) REVERT: G 1323 PHE cc_start: 0.6834 (t80) cc_final: 0.6512 (t80) REVERT: C 1260 ARG cc_start: 0.7643 (mtp180) cc_final: 0.7385 (ttt-90) REVERT: C 1299 MET cc_start: 0.4517 (tpt) cc_final: 0.4290 (tpt) REVERT: D 251 ASP cc_start: 0.8127 (m-30) cc_final: 0.7606 (t0) REVERT: D 345 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9132 (tp) REVERT: D 632 GLN cc_start: 0.8495 (tp-100) cc_final: 0.8276 (tp-100) REVERT: D 710 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7798 (mp10) REVERT: D 771 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7573 (mtt) REVERT: E 1096 ASN cc_start: 0.7068 (t0) cc_final: 0.6753 (t0) REVERT: I 1215 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8572 (tt) REVERT: I 1346 TRP cc_start: 0.5417 (t60) cc_final: 0.4642 (t60) REVERT: F 1260 ARG cc_start: 0.7592 (ttt-90) cc_final: 0.6913 (ptm160) REVERT: F 1274 ARG cc_start: 0.2800 (OUTLIER) cc_final: 0.2514 (mtt90) REVERT: F 1289 ARG cc_start: 0.7303 (mtt180) cc_final: 0.7101 (mtm-85) outliers start: 60 outliers final: 41 residues processed: 249 average time/residue: 0.3668 time to fit residues: 136.9629 Evaluate side-chains 241 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 195 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain B residue 1140 ASN Chi-restraints excluded: chain B residue 1192 MET Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1203 HIS Chi-restraints excluded: chain B residue 1205 ILE Chi-restraints excluded: chain G residue 1338 ASP Chi-restraints excluded: chain G residue 1350 VAL Chi-restraints excluded: chain C residue 1218 LEU Chi-restraints excluded: chain C residue 1273 VAL Chi-restraints excluded: chain C residue 1332 ILE Chi-restraints excluded: chain D residue 39 HIS Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain D residue 558 MET Chi-restraints excluded: chain D residue 595 MET Chi-restraints excluded: chain D residue 709 LEU Chi-restraints excluded: chain D residue 710 GLN Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 771 MET Chi-restraints excluded: chain D residue 772 ASP Chi-restraints excluded: chain D residue 786 VAL Chi-restraints excluded: chain E residue 1100 VAL Chi-restraints excluded: chain E residue 1112 ASN Chi-restraints excluded: chain E residue 1154 ILE Chi-restraints excluded: chain I residue 1215 LEU Chi-restraints excluded: chain I residue 1241 VAL Chi-restraints excluded: chain F residue 1221 MET Chi-restraints excluded: chain F residue 1239 HIS Chi-restraints excluded: chain F residue 1241 VAL Chi-restraints excluded: chain F residue 1274 ARG Chi-restraints excluded: chain F residue 1325 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 201 optimal weight: 0.0020 chunk 133 optimal weight: 0.9990 chunk 239 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 110 optimal weight: 0.0270 overall best weight: 0.8052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS A 810 ASN ** G1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1335 GLN ** C1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 742 HIS ** I1271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20838 Z= 0.204 Angle : 0.598 9.227 28298 Z= 0.302 Chirality : 0.045 0.205 3013 Planarity : 0.005 0.076 3657 Dihedral : 5.117 23.843 2740 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.86 % Allowed : 15.73 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.17), residues: 2508 helix: 0.77 (0.28), residues: 374 sheet: -1.11 (0.19), residues: 719 loop : -1.07 (0.17), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 375 HIS 0.007 0.001 HIS D 742 PHE 0.035 0.001 PHE E1182 TYR 0.017 0.001 TYR A 363 ARG 0.004 0.000 ARG E1099 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 210 time to evaluate : 2.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.8117 (t0) cc_final: 0.7569 (t70) REVERT: B 1129 PHE cc_start: 0.7419 (m-80) cc_final: 0.7103 (m-80) REVERT: B 1194 LEU cc_start: 0.8745 (mt) cc_final: 0.8462 (mt) REVERT: G 1228 PHE cc_start: 0.5625 (m-80) cc_final: 0.5103 (m-80) REVERT: G 1260 ARG cc_start: 0.7523 (mtm180) cc_final: 0.7260 (mtm180) REVERT: G 1286 MET cc_start: 0.5415 (ppp) cc_final: 0.5158 (ppp) REVERT: G 1323 PHE cc_start: 0.6827 (t80) cc_final: 0.6504 (t80) REVERT: C 1260 ARG cc_start: 0.7626 (mtp180) cc_final: 0.7374 (ttt-90) REVERT: C 1268 MET cc_start: 0.3816 (mmm) cc_final: 0.3279 (mtt) REVERT: C 1286 MET cc_start: 0.3959 (ptt) cc_final: 0.3411 (ptm) REVERT: C 1299 MET cc_start: 0.4468 (tpt) cc_final: 0.4181 (tpt) REVERT: D 251 ASP cc_start: 0.8108 (m-30) cc_final: 0.7588 (t0) REVERT: D 345 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9132 (tp) REVERT: D 632 GLN cc_start: 0.8463 (tp-100) cc_final: 0.8247 (tp-100) REVERT: D 684 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.6956 (mp10) REVERT: D 710 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7769 (mp10) REVERT: D 771 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7610 (mtt) REVERT: E 1096 ASN cc_start: 0.7065 (t0) cc_final: 0.6755 (t0) REVERT: E 1212 PHE cc_start: 0.7386 (m-80) cc_final: 0.7099 (m-80) REVERT: I 1215 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8600 (tt) REVERT: I 1346 TRP cc_start: 0.5513 (t60) cc_final: 0.4771 (t60) REVERT: F 1221 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7313 (mtp) REVERT: F 1260 ARG cc_start: 0.7604 (ttt-90) cc_final: 0.6905 (ptm160) REVERT: F 1274 ARG cc_start: 0.2757 (OUTLIER) cc_final: 0.2512 (mtt90) REVERT: F 1289 ARG cc_start: 0.7255 (mtt180) cc_final: 0.7042 (mtm-85) outliers start: 63 outliers final: 37 residues processed: 253 average time/residue: 0.3652 time to fit residues: 138.8622 Evaluate side-chains 240 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 196 time to evaluate : 2.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain B residue 1140 ASN Chi-restraints excluded: chain B residue 1192 MET Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1205 ILE Chi-restraints excluded: chain G residue 1338 ASP Chi-restraints excluded: chain G residue 1350 VAL Chi-restraints excluded: chain C residue 1218 LEU Chi-restraints excluded: chain C residue 1273 VAL Chi-restraints excluded: chain C residue 1332 ILE Chi-restraints excluded: chain D residue 39 HIS Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 433 SER Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain D residue 558 MET Chi-restraints excluded: chain D residue 595 MET Chi-restraints excluded: chain D residue 684 GLN Chi-restraints excluded: chain D residue 709 LEU Chi-restraints excluded: chain D residue 710 GLN Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 771 MET Chi-restraints excluded: chain D residue 772 ASP Chi-restraints excluded: chain D residue 786 VAL Chi-restraints excluded: chain E residue 1112 ASN Chi-restraints excluded: chain E residue 1154 ILE Chi-restraints excluded: chain I residue 1215 LEU Chi-restraints excluded: chain I residue 1241 VAL Chi-restraints excluded: chain F residue 1221 MET Chi-restraints excluded: chain F residue 1226 LEU Chi-restraints excluded: chain F residue 1239 HIS Chi-restraints excluded: chain F residue 1274 ARG Chi-restraints excluded: chain F residue 1325 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 162 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 187 optimal weight: 0.8980 chunk 217 optimal weight: 6.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS A 810 ASN ** G1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1335 GLN ** C1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20838 Z= 0.246 Angle : 0.612 9.485 28298 Z= 0.308 Chirality : 0.045 0.196 3013 Planarity : 0.005 0.069 3657 Dihedral : 5.076 23.781 2740 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.90 % Allowed : 16.36 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.17), residues: 2508 helix: 0.79 (0.28), residues: 374 sheet: -1.04 (0.19), residues: 721 loop : -1.08 (0.17), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP A 375 HIS 0.007 0.001 HIS B1165 PHE 0.027 0.001 PHE E1182 TYR 0.026 0.001 TYR C1251 ARG 0.007 0.000 ARG E1099 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 205 time to evaluate : 2.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.8131 (t0) cc_final: 0.7574 (t70) REVERT: A 771 MET cc_start: 0.7926 (mtt) cc_final: 0.7360 (mtt) REVERT: B 1129 PHE cc_start: 0.7429 (m-80) cc_final: 0.7159 (m-80) REVERT: G 1228 PHE cc_start: 0.5749 (m-80) cc_final: 0.5366 (m-80) REVERT: G 1260 ARG cc_start: 0.7560 (mtm180) cc_final: 0.7285 (mtm180) REVERT: G 1323 PHE cc_start: 0.6822 (t80) cc_final: 0.6469 (t80) REVERT: C 1251 TYR cc_start: 0.4702 (OUTLIER) cc_final: 0.3660 (t80) REVERT: C 1260 ARG cc_start: 0.7680 (mtp180) cc_final: 0.7415 (ttt-90) REVERT: D 251 ASP cc_start: 0.8132 (m-30) cc_final: 0.7610 (t0) REVERT: D 345 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9145 (tp) REVERT: D 632 GLN cc_start: 0.8469 (tp-100) cc_final: 0.8244 (tp-100) REVERT: D 710 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7755 (mp10) REVERT: D 771 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7543 (mtt) REVERT: E 1096 ASN cc_start: 0.7016 (t0) cc_final: 0.6697 (t0) REVERT: E 1117 PHE cc_start: 0.7336 (p90) cc_final: 0.6714 (p90) REVERT: E 1212 PHE cc_start: 0.7450 (m-80) cc_final: 0.7203 (m-80) REVERT: I 1215 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8568 (tt) REVERT: I 1346 TRP cc_start: 0.5525 (t60) cc_final: 0.4808 (t60) REVERT: F 1260 ARG cc_start: 0.7544 (ttt-90) cc_final: 0.6840 (ptm160) REVERT: F 1274 ARG cc_start: 0.2799 (OUTLIER) cc_final: 0.2589 (mtt90) REVERT: F 1289 ARG cc_start: 0.7252 (mtt180) cc_final: 0.7043 (mtm-85) outliers start: 64 outliers final: 44 residues processed: 247 average time/residue: 0.3441 time to fit residues: 128.3603 Evaluate side-chains 249 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 199 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain B residue 1117 PHE Chi-restraints excluded: chain B residue 1140 ASN Chi-restraints excluded: chain B residue 1192 MET Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1205 ILE Chi-restraints excluded: chain G residue 1235 VAL Chi-restraints excluded: chain G residue 1292 VAL Chi-restraints excluded: chain G residue 1338 ASP Chi-restraints excluded: chain G residue 1350 VAL Chi-restraints excluded: chain C residue 1218 LEU Chi-restraints excluded: chain C residue 1251 TYR Chi-restraints excluded: chain C residue 1273 VAL Chi-restraints excluded: chain C residue 1332 ILE Chi-restraints excluded: chain D residue 39 HIS Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain D residue 558 MET Chi-restraints excluded: chain D residue 595 MET Chi-restraints excluded: chain D residue 709 LEU Chi-restraints excluded: chain D residue 710 GLN Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 771 MET Chi-restraints excluded: chain D residue 772 ASP Chi-restraints excluded: chain D residue 786 VAL Chi-restraints excluded: chain E residue 1112 ASN Chi-restraints excluded: chain E residue 1154 ILE Chi-restraints excluded: chain I residue 1215 LEU Chi-restraints excluded: chain I residue 1241 VAL Chi-restraints excluded: chain F residue 1226 LEU Chi-restraints excluded: chain F residue 1239 HIS Chi-restraints excluded: chain F residue 1241 VAL Chi-restraints excluded: chain F residue 1274 ARG Chi-restraints excluded: chain F residue 1325 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 8.9990 chunk 208 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 174 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 201 optimal weight: 4.9990 chunk 210 optimal weight: 8.9990 chunk 221 optimal weight: 0.0050 chunk 146 optimal weight: 2.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS A 507 ASN A 810 ASN ** G1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1335 GLN ** C1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 525 HIS I1271 GLN ** I1335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20838 Z= 0.247 Angle : 0.612 9.171 28298 Z= 0.308 Chirality : 0.045 0.298 3013 Planarity : 0.005 0.077 3657 Dihedral : 5.053 23.601 2740 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.86 % Allowed : 16.23 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.21 (0.17), residues: 2508 helix: 0.79 (0.28), residues: 374 sheet: -1.07 (0.19), residues: 717 loop : -1.07 (0.17), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP A 375 HIS 0.010 0.001 HIS A 812 PHE 0.027 0.001 PHE I1228 TYR 0.020 0.001 TYR C1251 ARG 0.007 0.000 ARG E1099 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 206 time to evaluate : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.8129 (t0) cc_final: 0.7576 (t70) REVERT: A 771 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7463 (mtt) REVERT: B 1129 PHE cc_start: 0.7465 (m-80) cc_final: 0.7213 (m-80) REVERT: G 1228 PHE cc_start: 0.5731 (m-80) cc_final: 0.5344 (m-80) REVERT: G 1260 ARG cc_start: 0.7552 (mtm180) cc_final: 0.7276 (mtm180) REVERT: G 1323 PHE cc_start: 0.6808 (t80) cc_final: 0.6456 (t80) REVERT: C 1251 TYR cc_start: 0.4654 (OUTLIER) cc_final: 0.3438 (t80) REVERT: C 1260 ARG cc_start: 0.7685 (mtp180) cc_final: 0.7451 (ttt-90) REVERT: C 1268 MET cc_start: 0.3640 (mmm) cc_final: 0.3103 (mtt) REVERT: D 251 ASP cc_start: 0.8155 (m-30) cc_final: 0.7623 (t0) REVERT: D 345 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9144 (tp) REVERT: D 632 GLN cc_start: 0.8476 (tp-100) cc_final: 0.8251 (tp-100) REVERT: D 710 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7812 (mp10) REVERT: D 771 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7582 (mtt) REVERT: E 1096 ASN cc_start: 0.7001 (t0) cc_final: 0.6700 (t0) REVERT: E 1117 PHE cc_start: 0.7279 (p90) cc_final: 0.6579 (p90) REVERT: I 1215 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8549 (tt) REVERT: I 1346 TRP cc_start: 0.5450 (t60) cc_final: 0.4778 (t60) REVERT: F 1221 MET cc_start: 0.7116 (mtp) cc_final: 0.6725 (mmm) REVERT: F 1260 ARG cc_start: 0.7506 (ttt-90) cc_final: 0.6805 (ptm160) outliers start: 63 outliers final: 47 residues processed: 249 average time/residue: 0.3474 time to fit residues: 129.9537 Evaluate side-chains 251 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 198 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain B residue 1117 PHE Chi-restraints excluded: chain B residue 1140 ASN Chi-restraints excluded: chain B residue 1192 MET Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1205 ILE Chi-restraints excluded: chain G residue 1292 VAL Chi-restraints excluded: chain G residue 1338 ASP Chi-restraints excluded: chain G residue 1350 VAL Chi-restraints excluded: chain C residue 1218 LEU Chi-restraints excluded: chain C residue 1251 TYR Chi-restraints excluded: chain C residue 1273 VAL Chi-restraints excluded: chain C residue 1332 ILE Chi-restraints excluded: chain D residue 39 HIS Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 394 GLU Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain D residue 558 MET Chi-restraints excluded: chain D residue 595 MET Chi-restraints excluded: chain D residue 709 LEU Chi-restraints excluded: chain D residue 710 GLN Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 767 THR Chi-restraints excluded: chain D residue 771 MET Chi-restraints excluded: chain D residue 772 ASP Chi-restraints excluded: chain D residue 786 VAL Chi-restraints excluded: chain E residue 1112 ASN Chi-restraints excluded: chain E residue 1136 LEU Chi-restraints excluded: chain E residue 1154 ILE Chi-restraints excluded: chain I residue 1215 LEU Chi-restraints excluded: chain I residue 1241 VAL Chi-restraints excluded: chain F residue 1217 VAL Chi-restraints excluded: chain F residue 1226 LEU Chi-restraints excluded: chain F residue 1239 HIS Chi-restraints excluded: chain F residue 1241 VAL Chi-restraints excluded: chain F residue 1325 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.5405 > 50: distance: 94 - 207: 35.587 distance: 97 - 204: 31.198 distance: 110 - 184: 25.491 distance: 113 - 181: 30.578 distance: 144 - 150: 28.309 distance: 150 - 151: 14.137 distance: 151 - 152: 36.053 distance: 151 - 154: 66.154 distance: 152 - 153: 39.725 distance: 152 - 159: 23.909 distance: 154 - 155: 56.037 distance: 155 - 156: 42.420 distance: 156 - 157: 40.299 distance: 156 - 158: 43.495 distance: 159 - 160: 20.142 distance: 160 - 161: 39.036 distance: 160 - 163: 50.406 distance: 161 - 166: 37.786 distance: 163 - 164: 3.672 distance: 163 - 165: 54.866 distance: 166 - 167: 57.119 distance: 167 - 168: 34.006 distance: 167 - 170: 25.878 distance: 168 - 169: 51.465 distance: 168 - 174: 50.978 distance: 170 - 171: 56.432 distance: 171 - 172: 54.122 distance: 171 - 173: 36.986 distance: 174 - 175: 22.662 distance: 175 - 176: 29.359 distance: 175 - 178: 24.479 distance: 176 - 177: 40.304 distance: 176 - 181: 47.072 distance: 178 - 179: 42.484 distance: 178 - 180: 47.718 distance: 181 - 182: 28.225 distance: 182 - 183: 25.767 distance: 182 - 185: 23.290 distance: 183 - 184: 19.124 distance: 183 - 195: 11.581 distance: 185 - 186: 5.794 distance: 186 - 187: 10.208 distance: 186 - 188: 19.850 distance: 187 - 189: 23.560 distance: 188 - 190: 14.425 distance: 189 - 190: 3.841 distance: 190 - 192: 5.867 distance: 191 - 193: 11.870 distance: 192 - 194: 6.305 distance: 195 - 196: 20.638 distance: 196 - 197: 33.623 distance: 196 - 199: 42.480 distance: 197 - 198: 48.462 distance: 197 - 204: 20.373 distance: 199 - 200: 40.960 distance: 200 - 201: 30.622 distance: 201 - 202: 17.340 distance: 201 - 203: 17.210 distance: 204 - 205: 25.427 distance: 205 - 206: 29.039 distance: 205 - 208: 41.956 distance: 206 - 207: 37.216 distance: 206 - 209: 43.382 distance: 209 - 210: 18.223 distance: 210 - 211: 10.825 distance: 210 - 213: 20.142 distance: 211 - 212: 21.671 distance: 211 - 217: 43.072 distance: 213 - 214: 34.523 distance: 214 - 215: 18.730 distance: 214 - 216: 26.961 distance: 217 - 218: 25.568 distance: 218 - 219: 48.931 distance: 218 - 221: 22.679 distance: 219 - 220: 64.517 distance: 219 - 224: 29.106 distance: 221 - 222: 35.331 distance: 221 - 223: 18.600 distance: 224 - 225: 61.951 distance: 225 - 226: 47.100 distance: 225 - 228: 50.961 distance: 226 - 227: 53.696 distance: 226 - 233: 35.889 distance: 228 - 229: 54.632 distance: 229 - 230: 37.662 distance: 230 - 231: 55.524 distance: 231 - 232: 63.210