Starting phenix.real_space_refine on Thu Aug 8 03:07:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klb_0705/08_2024/6klb_0705_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klb_0705/08_2024/6klb_0705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klb_0705/08_2024/6klb_0705.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klb_0705/08_2024/6klb_0705.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klb_0705/08_2024/6klb_0705_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klb_0705/08_2024/6klb_0705_neut.cif" } resolution = 4.1 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= 0.001 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: 6 Type Number sf(0) Gaussians P 50 5.49 5 Mg 4 5.21 5 S 62 5.16 5 C 13519 2.51 5 N 3518 2.21 5 O 4231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 548": "NH1" <-> "NH2" Residue "A ARG 737": "NH1" <-> "NH2" Residue "A ARG 883": "NH1" <-> "NH2" Residue "A ARG 887": "NH1" <-> "NH2" Residue "A ARG 1112": "NH1" <-> "NH2" Residue "B ARG 155": "NH1" <-> "NH2" Residue "B ARG 217": "NH1" <-> "NH2" Residue "C ARG 155": "NH1" <-> "NH2" Residue "C ARG 217": "NH1" <-> "NH2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 548": "NH1" <-> "NH2" Residue "D ARG 737": "NH1" <-> "NH2" Residue "D ARG 883": "NH1" <-> "NH2" Residue "D ARG 887": "NH1" <-> "NH2" Residue "D ARG 1112": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 21384 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 9206 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1118, 9197 Classifications: {'peptide': 1118} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 21, 'TRANS': 1096} Chain breaks: 3 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Conformer: "B" Number of residues, atoms: 1118, 9197 Classifications: {'peptide': 1118} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 21, 'TRANS': 1096} Chain breaks: 3 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 bond proxies already assigned to first conformer: 9369 Chain: "B" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 967 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "C" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 967 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "D" Number of atoms: 9171 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1115, 9162 Classifications: {'peptide': 1115} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 1093} Chain breaks: 3 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 1115, 9162 Classifications: {'peptide': 1115} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 1093} Chain breaks: 3 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 9332 Chain: "E" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 529 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 7, 'rna3p_pyr': 9} Link IDs: {'rna2p': 9, 'rna3p': 15} Chain: "G" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 529 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 7, 'rna3p_pyr': 9} Link IDs: {'rna2p': 9, 'rna3p': 15} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ALYS A 775 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 775 " occ=0.50 residue: pdb=" N ALYS D 775 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS D 775 " occ=0.50 Time building chain proxies: 21.15, per 1000 atoms: 0.99 Number of scatterers: 21384 At special positions: 0 Unit cell: (129.6, 185.76, 160.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 62 16.00 P 50 15.00 Mg 4 11.99 O 4231 8.00 N 3518 7.00 C 13519 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS C 131 " distance=2.02 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: 8.78 Conformation dependent library (CDL) restraints added in 6.4 seconds 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4730 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 23 sheets defined 45.5% alpha, 9.5% beta 10 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 7.16 Creating SS restraints... Processing helix chain 'A' and resid 25 through 33 removed outlier: 4.096A pdb=" N GLU A 29 " --> pdb=" O GLY A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 68 removed outlier: 4.463A pdb=" N SER A 68 " --> pdb=" O ASP A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 82 removed outlier: 3.934A pdb=" N TYR A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 111 removed outlier: 3.657A pdb=" N GLU A 93 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 148 through 160 Processing helix chain 'A' and resid 170 through 193 Processing helix chain 'A' and resid 203 through 210 Processing helix chain 'A' and resid 217 through 220 removed outlier: 3.586A pdb=" N PHE A 220 " --> pdb=" O GLU A 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 217 through 220' Processing helix chain 'A' and resid 221 through 226 removed outlier: 3.961A pdb=" N PHE A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 221 through 226' Processing helix chain 'A' and resid 230 through 242 removed outlier: 3.542A pdb=" N ILE A 234 " --> pdb=" O THR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 263 removed outlier: 3.737A pdb=" N TYR A 258 " --> pdb=" O GLY A 254 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 305 removed outlier: 3.900A pdb=" N VAL A 300 " --> pdb=" O SER A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 330 Processing helix chain 'A' and resid 342 through 352 removed outlier: 3.845A pdb=" N THR A 346 " --> pdb=" O PRO A 342 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 370 Processing helix chain 'A' and resid 378 through 393 removed outlier: 4.086A pdb=" N GLY A 393 " --> pdb=" O PHE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 403 Processing helix chain 'A' and resid 409 through 431 removed outlier: 3.598A pdb=" N SER A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 436 removed outlier: 4.091A pdb=" N PHE A 436 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 472 Processing helix chain 'A' and resid 485 through 512 removed outlier: 4.015A pdb=" N ASP A 489 " --> pdb=" O SER A 485 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR A 512 " --> pdb=" O ARG A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 566 removed outlier: 3.954A pdb=" N LEU A 566 " --> pdb=" O ALA A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 697 Processing helix chain 'A' and resid 706 through 710 removed outlier: 3.830A pdb=" N PHE A 709 " --> pdb=" O ASN A 706 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER A 710 " --> pdb=" O LYS A 707 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 706 through 710' Processing helix chain 'A' and resid 719 through 726 removed outlier: 3.604A pdb=" N LEU A 726 " --> pdb=" O MET A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 790 removed outlier: 3.563A pdb=" N PHE A 789 " --> pdb=" O ASP A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 823 removed outlier: 3.896A pdb=" N GLU A 815 " --> pdb=" O LYS A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 885 Processing helix chain 'A' and resid 889 through 919 Processing helix chain 'A' and resid 939 through 954 removed outlier: 3.594A pdb=" N TYR A 943 " --> pdb=" O GLU A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1030 Processing helix chain 'A' and resid 1050 through 1052 No H-bonds generated for 'chain 'A' and resid 1050 through 1052' Processing helix chain 'A' and resid 1091 through 1100 Processing helix chain 'A' and resid 1120 through 1136 removed outlier: 4.407A pdb=" N TYR A1124 " --> pdb=" O ASP A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1200 Processing helix chain 'A' and resid 1203 through 1208 removed outlier: 3.761A pdb=" N LEU A1206 " --> pdb=" O ASP A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1225 Processing helix chain 'B' and resid 118 through 149 removed outlier: 3.603A pdb=" N LEU B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 170 removed outlier: 3.822A pdb=" N LEU B 170 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 removed outlier: 3.855A pdb=" N ARG B 203 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU B 204 " --> pdb=" O THR B 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 200 through 204' Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.870A pdb=" N LEU B 232 " --> pdb=" O VAL B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 149 Processing helix chain 'C' and resid 166 through 170 removed outlier: 3.958A pdb=" N LEU C 170 " --> pdb=" O PRO C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 removed outlier: 4.060A pdb=" N ARG C 203 " --> pdb=" O SER C 200 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU C 204 " --> pdb=" O THR C 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 200 through 204' Processing helix chain 'C' and resid 227 through 232 Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 37 through 66 Processing helix chain 'D' and resid 73 through 82 removed outlier: 3.737A pdb=" N TYR D 77 " --> pdb=" O ASN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 111 Processing helix chain 'D' and resid 120 through 126 removed outlier: 4.069A pdb=" N ILE D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 131 removed outlier: 3.808A pdb=" N GLU D 130 " --> pdb=" O THR D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 142 Processing helix chain 'D' and resid 148 through 162 removed outlier: 4.014A pdb=" N PHE D 162 " --> pdb=" O ARG D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 193 removed outlier: 3.532A pdb=" N LYS D 192 " --> pdb=" O ASP D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 211 removed outlier: 3.581A pdb=" N LYS D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 220 removed outlier: 3.719A pdb=" N PHE D 220 " --> pdb=" O GLU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 226 removed outlier: 4.041A pdb=" N PHE D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN D 226 " --> pdb=" O GLY D 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 221 through 226' Processing helix chain 'D' and resid 230 through 242 Processing helix chain 'D' and resid 255 through 263 removed outlier: 4.483A pdb=" N ASN D 263 " --> pdb=" O ILE D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 305 removed outlier: 3.565A pdb=" N VAL D 300 " --> pdb=" O SER D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 330 Processing helix chain 'D' and resid 342 through 352 Processing helix chain 'D' and resid 355 through 370 removed outlier: 4.249A pdb=" N ARG D 359 " --> pdb=" O TRP D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 393 removed outlier: 3.959A pdb=" N GLY D 393 " --> pdb=" O PHE D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 404 Processing helix chain 'D' and resid 409 through 431 removed outlier: 3.656A pdb=" N SER D 431 " --> pdb=" O LYS D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 472 Processing helix chain 'D' and resid 485 through 512 removed outlier: 4.239A pdb=" N ASP D 489 " --> pdb=" O SER D 485 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N THR D 512 " --> pdb=" O ARG D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 564 removed outlier: 4.173A pdb=" N LYS D 564 " --> pdb=" O LYS D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 697 Processing helix chain 'D' and resid 718 through 726 removed outlier: 3.823A pdb=" N MET D 722 " --> pdb=" O ASN D 718 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU D 726 " --> pdb=" O MET D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 786 through 790 removed outlier: 3.727A pdb=" N PHE D 789 " --> pdb=" O ASP D 786 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 823 removed outlier: 3.581A pdb=" N GLU D 815 " --> pdb=" O LYS D 811 " (cutoff:3.500A) Processing helix chain 'D' and resid 872 through 885 Processing helix chain 'D' and resid 889 through 918 Processing helix chain 'D' and resid 939 through 954 removed outlier: 3.725A pdb=" N TYR D 943 " --> pdb=" O GLU D 939 " (cutoff:3.500A) Processing helix chain 'D' and resid 982 through 986 removed outlier: 3.822A pdb=" N MET D 986 " --> pdb=" O PHE D 983 " (cutoff:3.500A) Processing helix chain 'D' and resid 1021 through 1030 Processing helix chain 'D' and resid 1091 through 1101 Processing helix chain 'D' and resid 1114 through 1118 removed outlier: 3.944A pdb=" N GLN D1118 " --> pdb=" O LEU D1115 " (cutoff:3.500A) Processing helix chain 'D' and resid 1121 through 1136 Processing helix chain 'D' and resid 1178 through 1201 Processing helix chain 'D' and resid 1203 through 1208 Processing helix chain 'D' and resid 1215 through 1225 Processing sheet with id=AA1, first strand: chain 'A' and resid 520 through 522 removed outlier: 3.689A pdb=" N TYR A 705 " --> pdb=" O LYS A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 520 through 522 Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 244 removed outlier: 3.586A pdb=" N PHE A 244 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 252 " --> pdb=" O PHE A 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 337 through 339 removed outlier: 3.904A pdb=" N PHE A 395 " --> pdb=" O VAL A 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 580 through 581 Processing sheet with id=AA6, first strand: chain 'A' and resid 765 through 766 Processing sheet with id=AA7, first strand: chain 'A' and resid 827 through 828 Processing sheet with id=AA8, first strand: chain 'A' and resid 858 through 863 Processing sheet with id=AA9, first strand: chain 'A' and resid 924 through 925 removed outlier: 6.937A pdb=" N LEU A 924 " --> pdb=" O ILE A 996 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 1034 through 1037 Processing sheet with id=AB2, first strand: chain 'A' and resid 1070 through 1073 Processing sheet with id=AB3, first strand: chain 'B' and resid 157 through 161 Processing sheet with id=AB4, first strand: chain 'B' and resid 185 through 188 Processing sheet with id=AB5, first strand: chain 'C' and resid 180 through 181 removed outlier: 4.252A pdb=" N GLU C 180 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASN C 157 " --> pdb=" O VAL C 213 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 520 through 522 Processing sheet with id=AB7, first strand: chain 'D' and resid 520 through 522 Processing sheet with id=AB8, first strand: chain 'D' and resid 337 through 339 removed outlier: 3.907A pdb=" N PHE D 395 " --> pdb=" O VAL D 338 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 580 through 582 Processing sheet with id=AC1, first strand: chain 'D' and resid 758 through 759 Processing sheet with id=AC2, first strand: chain 'D' and resid 828 through 831 Processing sheet with id=AC3, first strand: chain 'D' and resid 858 through 863 Processing sheet with id=AC4, first strand: chain 'D' and resid 1031 through 1037 removed outlier: 6.465A pdb=" N PHE D1031 " --> pdb=" O ASP D1048 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ASP D1048 " --> pdb=" O PHE D1031 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET D1035 " --> pdb=" O GLU D1044 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU D1044 " --> pdb=" O MET D1035 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL D1037 " --> pdb=" O LEU D1042 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU D1042 " --> pdb=" O VAL D1037 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 1071 through 1073 895 hydrogen bonds defined for protein. 2547 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 7.34 Time building geometry restraints manager: 9.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4352 1.33 - 1.45: 5505 1.45 - 1.58: 11836 1.58 - 1.70: 98 1.70 - 1.83: 102 Bond restraints: 21893 Sorted by residual: bond pdb=" N GLU B 219 " pdb=" CA GLU B 219 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.41e+00 bond pdb=" N ASP B 218 " pdb=" CA ASP B 218 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.89e+00 bond pdb=" C ASP C 192 " pdb=" N GLN C 193 " ideal model delta sigma weight residual 1.324 1.356 -0.032 1.38e-02 5.25e+03 5.49e+00 bond pdb=" C LYS D1101 " pdb=" O LYS D1101 " ideal model delta sigma weight residual 1.234 1.205 0.030 1.33e-02 5.65e+03 4.92e+00 bond pdb=" C VAL D 828 " pdb=" N ILE D 829 " ideal model delta sigma weight residual 1.331 1.357 -0.026 1.28e-02 6.10e+03 4.16e+00 ... (remaining 21888 not shown) Histogram of bond angle deviations from ideal: 100.14 - 106.94: 671 106.94 - 113.74: 11799 113.74 - 120.54: 9111 120.54 - 127.34: 7892 127.34 - 134.14: 218 Bond angle restraints: 29691 Sorted by residual: angle pdb=" N ALA A 920 " pdb=" CA ALA A 920 " pdb=" C ALA A 920 " ideal model delta sigma weight residual 109.07 124.22 -15.15 1.61e+00 3.86e-01 8.86e+01 angle pdb=" N HIS C 190 " pdb=" CA HIS C 190 " pdb=" C HIS C 190 " ideal model delta sigma weight residual 114.75 103.63 11.12 1.26e+00 6.30e-01 7.79e+01 angle pdb=" N ASN A 849 " pdb=" CA ASN A 849 " pdb=" C ASN A 849 " ideal model delta sigma weight residual 109.24 121.32 -12.08 1.67e+00 3.59e-01 5.24e+01 angle pdb=" N ILE A 922 " pdb=" CA ILE A 922 " pdb=" C ILE A 922 " ideal model delta sigma weight residual 109.45 118.57 -9.12 1.39e+00 5.18e-01 4.31e+01 angle pdb=" C LYS A 267 " pdb=" N GLN A 268 " pdb=" CA GLN A 268 " ideal model delta sigma weight residual 121.54 133.03 -11.49 1.91e+00 2.74e-01 3.62e+01 ... (remaining 29686 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 13181 35.58 - 71.16: 165 71.16 - 106.73: 13 106.73 - 142.31: 0 142.31 - 177.89: 6 Dihedral angle restraints: 13365 sinusoidal: 6031 harmonic: 7334 Sorted by residual: dihedral pdb=" O4' C G 21 " pdb=" C1' C G 21 " pdb=" N1 C G 21 " pdb=" C2 C G 21 " ideal model delta sinusoidal sigma weight residual -128.00 49.89 -177.89 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U G 14 " pdb=" C1' U G 14 " pdb=" N1 U G 14 " pdb=" C2 U G 14 " ideal model delta sinusoidal sigma weight residual -128.00 49.12 -177.12 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U E 14 " pdb=" C1' U E 14 " pdb=" N1 U E 14 " pdb=" C2 U E 14 " ideal model delta sinusoidal sigma weight residual -128.00 48.81 -176.81 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 13362 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3021 0.098 - 0.196: 209 0.196 - 0.294: 12 0.294 - 0.392: 2 0.392 - 0.490: 2 Chirality restraints: 3246 Sorted by residual: chirality pdb=" CA ALA A 920 " pdb=" N ALA A 920 " pdb=" C ALA A 920 " pdb=" CB ALA A 920 " both_signs ideal model delta sigma weight residual False 2.48 1.99 0.49 2.00e-01 2.50e+01 6.01e+00 chirality pdb=" CA GLU B 219 " pdb=" N GLU B 219 " pdb=" C GLU B 219 " pdb=" CB GLU B 219 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" CA ASN A 849 " pdb=" N ASN A 849 " pdb=" C ASN A 849 " pdb=" CB ASN A 849 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 3243 not shown) Planarity restraints: 3615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 187 " -0.027 2.00e-02 2.50e+03 5.35e-02 2.87e+01 pdb=" C ARG C 187 " 0.093 2.00e-02 2.50e+03 pdb=" O ARG C 187 " -0.035 2.00e-02 2.50e+03 pdb=" N TYR C 188 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D1101 " -0.021 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C LYS D1101 " 0.071 2.00e-02 2.50e+03 pdb=" O LYS D1101 " -0.027 2.00e-02 2.50e+03 pdb=" N TYR D1102 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 919 " 0.016 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C ASP A 919 " -0.058 2.00e-02 2.50e+03 pdb=" O ASP A 919 " 0.023 2.00e-02 2.50e+03 pdb=" N ALA A 920 " 0.019 2.00e-02 2.50e+03 ... (remaining 3612 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 194 2.59 - 3.17: 16997 3.17 - 3.75: 31314 3.75 - 4.32: 43929 4.32 - 4.90: 69312 Nonbonded interactions: 161746 Sorted by model distance: nonbonded pdb="MG MG G 101 " pdb=" O HOH G 204 " model vdw 2.015 2.170 nonbonded pdb="MG MG E1302 " pdb=" O HOH E1405 " model vdw 2.016 2.170 nonbonded pdb="MG MG G 101 " pdb=" O HOH G 201 " model vdw 2.030 2.170 nonbonded pdb="MG MG E1302 " pdb=" O HOH E1403 " model vdw 2.031 2.170 nonbonded pdb="MG MG G 101 " pdb=" O HOH G 202 " model vdw 2.036 2.170 ... (remaining 161741 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 584 or resid 680 through 774 or resid 776 throug \ h 993 or (resid 994 and (name N or name CA or name C or name O or name CB )) or \ resid 995 through 1227)) selection = (chain 'D' and (resid 1 through 774 or resid 776 through 1227)) } ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'E' and (resid 1 through 25 or resid 1301)) selection = chain 'G' } 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=0.50 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: 9.740 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: 0.940 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 74.580 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5463 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21893 Z= 0.233 Angle : 0.901 15.152 29691 Z= 0.511 Chirality : 0.054 0.490 3246 Planarity : 0.006 0.076 3615 Dihedral : 12.494 177.889 8632 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.99 % Favored : 90.76 % Rotamer: Outliers : 0.31 % Allowed : 2.24 % Favored : 97.45 % Cbeta Deviations : 0.04 % 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: -5.01 (0.12), residues: 2453 helix: -3.34 (0.10), residues: 984 sheet: -2.14 (0.31), residues: 226 loop : -3.59 (0.13), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 362 HIS 0.012 0.002 HIS A 909 PHE 0.027 0.002 PHE A 709 TYR 0.019 0.002 TYR A 553 ARG 0.008 0.001 ARG B 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 2243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 632 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.6875 (mtpt) cc_final: 0.6429 (mmtm) REVERT: A 132 LEU cc_start: 0.7316 (mt) cc_final: 0.6950 (mt) REVERT: A 479 GLU cc_start: 0.7494 (mm-30) cc_final: 0.6000 (pm20) REVERT: A 746 MET cc_start: 0.4124 (tmt) cc_final: 0.3790 (tpt) REVERT: A 836 ARG cc_start: 0.5905 (mtt-85) cc_final: 0.4677 (mtt180) REVERT: A 914 LEU cc_start: 0.8407 (mt) cc_final: 0.8195 (mt) REVERT: A 1167 TYR cc_start: 0.4808 (m-80) cc_final: 0.4510 (m-80) REVERT: C 152 TYR cc_start: 0.4799 (m-80) cc_final: 0.4592 (m-80) REVERT: C 217 ARG cc_start: 0.5399 (OUTLIER) cc_final: 0.4866 (ptt90) REVERT: D 124 ILE cc_start: 0.7933 (pt) cc_final: 0.7371 (pt) REVERT: D 257 GLU cc_start: 0.7424 (mp0) cc_final: 0.6987 (tm-30) REVERT: D 387 LYS cc_start: 0.8323 (mmtm) cc_final: 0.8052 (mtpt) REVERT: D 429 TYR cc_start: 0.6482 (m-10) cc_final: 0.6274 (m-80) REVERT: D 836 ARG cc_start: 0.6943 (mtt-85) cc_final: 0.6712 (tpm170) REVERT: D 841 ILE cc_start: 0.7900 (mm) cc_final: 0.7584 (mt) REVERT: D 957 MET cc_start: 0.6061 (ttp) cc_final: 0.5675 (tpt) outliers start: 7 outliers final: 1 residues processed: 638 average time/residue: 0.3875 time to fit residues: 357.2341 Evaluate side-chains 304 residues out of total 2243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 302 time to evaluate : 3.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.5980 chunk 187 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 194 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 144 optimal weight: 6.9990 chunk 225 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 268 GLN A 370 HIS A 762 ASN ** A 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 GLN A 889 ASN A 895 ASN A 989 GLN ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1139 ASN A1166 ASN B 181 GLN C 181 GLN D 63 ASN D 100 ASN D 186 ASN ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 509 ASN D 735 GLN D 762 ASN ** D 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 803 ASN D 837 ASN D 857 ASN D 888 GLN D1223 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5772 moved from start: 0.3488 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: