Starting phenix.real_space_refine on Tue Mar 19 23:26:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eos_28466/03_2024/8eos_28466_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eos_28466/03_2024/8eos_28466.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eos_28466/03_2024/8eos_28466_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eos_28466/03_2024/8eos_28466_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eos_28466/03_2024/8eos_28466_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eos_28466/03_2024/8eos_28466.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eos_28466/03_2024/8eos_28466.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eos_28466/03_2024/8eos_28466_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eos_28466/03_2024/8eos_28466_trim_updated.pdb" } resolution = 3.1 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= 0.001 sd= 0.059 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 90 5.49 5 Mg 2 5.21 5 S 87 5.16 5 C 15759 2.51 5 N 4564 2.21 5 O 5102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1011": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1083": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 749": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1077": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25606 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1724 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "B" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1765 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 221} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 8686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1123, 8686 Classifications: {'peptide': 1123} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 60, 'TRANS': 1061} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 9982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1276, 9982 Classifications: {'peptide': 1276} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1215} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 76} Chain: "G" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 968 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "T" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 774 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "N" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 737 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain breaks: 1 Chain: "R" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 288 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 1} Link IDs: {'rna2p': 4, 'rna3p': 8} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'2TM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19226 SG CYS D 891 75.984 23.919 87.353 1.00 56.97 S ATOM 19793 SG CYS D 968 74.786 27.253 88.760 1.00 44.72 S ATOM 19835 SG CYS D 975 76.375 27.133 85.308 1.00 45.87 S ATOM 19853 SG CYS D 978 72.979 25.745 85.784 1.00 57.84 S ATOM 12664 SG CYS D 60 108.078 79.295 116.139 1.00121.58 S ATOM 12682 SG CYS D 62 109.245 82.270 118.193 1.00128.23 S ATOM 12791 SG CYS D 75 110.252 78.449 118.868 1.00127.60 S ATOM 12817 SG CYS D 78 106.692 80.099 119.556 1.00132.10 S Time building chain proxies: 14.11, per 1000 atoms: 0.55 Number of scatterers: 25606 At special positions: 0 Unit cell: (125.28, 138.33, 200.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 87 16.00 P 90 15.00 Mg 2 11.99 O 5102 8.00 N 4564 7.00 C 15759 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: 10.60 Conformation dependent library (CDL) restraints added in 4.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 968 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 891 " pdb=" ZN D2004 " pdb="ZN ZN D2004 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2004 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2004 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2004 " - pdb=" SG CYS D 75 " Number of angles added : 12 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5640 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 103 helices and 31 sheets defined 32.3% alpha, 12.5% beta 33 base pairs and 64 stacking pairs defined. Time for finding SS restraints: 12.41 Creating SS restraints... Processing helix chain 'A' and resid 32 through 42 Processing helix chain 'A' and resid 73 through 82 removed outlier: 4.333A pdb=" N SER A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 109 No H-bonds generated for 'chain 'A' and resid 107 through 109' Processing helix chain 'A' and resid 184 through 186 No H-bonds generated for 'chain 'A' and resid 184 through 186' Processing helix chain 'A' and resid 204 through 220 removed outlier: 3.627A pdb=" N LEU A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'B' and resid 32 through 44 removed outlier: 4.265A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 82 removed outlier: 3.629A pdb=" N SER B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 109 No H-bonds generated for 'chain 'B' and resid 107 through 109' Processing helix chain 'B' and resid 204 through 211 Processing helix chain 'B' and resid 216 through 225 removed outlier: 4.347A pdb=" N LEU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 65 removed outlier: 4.405A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE C 61 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 86 through 93 Processing helix chain 'C' and resid 119 through 125 Processing helix chain 'C' and resid 234 through 240 Processing helix chain 'C' and resid 247 through 251 Processing helix chain 'C' and resid 256 through 263 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 311 through 320 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 381 through 405 removed outlier: 3.670A pdb=" N GLN C 388 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG C 398 " --> pdb=" O SER C 394 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL C 399 " --> pdb=" O ARG C 395 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET C 404 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 417 No H-bonds generated for 'chain 'C' and resid 414 through 417' Processing helix chain 'C' and resid 421 through 431 Processing helix chain 'C' and resid 445 through 451 Processing helix chain 'C' and resid 477 through 479 No H-bonds generated for 'chain 'C' and resid 477 through 479' Processing helix chain 'C' and resid 533 through 538 removed outlier: 4.210A pdb=" N ARG C 538 " --> pdb=" O ASP C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 593 No H-bonds generated for 'chain 'C' and resid 591 through 593' Processing helix chain 'C' and resid 597 through 599 No H-bonds generated for 'chain 'C' and resid 597 through 599' Processing helix chain 'C' and resid 602 through 613 removed outlier: 4.250A pdb=" N ARG C 613 " --> pdb=" O ALA C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 636 Processing helix chain 'C' and resid 740 through 743 No H-bonds generated for 'chain 'C' and resid 740 through 743' Processing helix chain 'C' and resid 901 through 903 No H-bonds generated for 'chain 'C' and resid 901 through 903' Processing helix chain 'C' and resid 929 through 942 Processing helix chain 'C' and resid 954 through 956 No H-bonds generated for 'chain 'C' and resid 954 through 956' Processing helix chain 'C' and resid 982 through 990 removed outlier: 3.783A pdb=" N SER C 990 " --> pdb=" O GLN C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1037 through 1039 No H-bonds generated for 'chain 'C' and resid 1037 through 1039' Processing helix chain 'C' and resid 1070 through 1079 Processing helix chain 'C' and resid 1082 through 1090 removed outlier: 3.680A pdb=" N GLN C1086 " --> pdb=" O ALA C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1098 through 1108 Processing helix chain 'C' and resid 1119 through 1130 Processing helix chain 'D' and resid 4 through 6 No H-bonds generated for 'chain 'D' and resid 4 through 6' Processing helix chain 'D' and resid 17 through 23 Processing helix chain 'D' and resid 49 through 52 No H-bonds generated for 'chain 'D' and resid 49 through 52' Processing helix chain 'D' and resid 68 through 70 No H-bonds generated for 'chain 'D' and resid 68 through 70' Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.622A pdb=" N ARG D 88 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 118 No H-bonds generated for 'chain 'D' and resid 115 through 118' Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 141 through 184 removed outlier: 6.206A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 227 removed outlier: 3.949A pdb=" N ASP D 192 " --> pdb=" O GLY D 188 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ALA D 193 " --> pdb=" O ALA D 189 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS D 196 " --> pdb=" O ASP D 192 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 247 Processing helix chain 'D' and resid 258 through 267 Processing helix chain 'D' and resid 270 through 282 Processing helix chain 'D' and resid 287 through 304 removed outlier: 3.940A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 324 No H-bonds generated for 'chain 'D' and resid 322 through 324' Processing helix chain 'D' and resid 340 through 359 removed outlier: 3.539A pdb=" N TYR D 344 " --> pdb=" O LEU D 340 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG D 345 " --> pdb=" O ASN D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 382 Processing helix chain 'D' and resid 402 through 405 Processing helix chain 'D' and resid 412 through 415 No H-bonds generated for 'chain 'D' and resid 412 through 415' Processing helix chain 'D' and resid 445 through 451 Processing helix chain 'D' and resid 453 through 462 Processing helix chain 'D' and resid 469 through 478 Processing helix chain 'D' and resid 487 through 490 No H-bonds generated for 'chain 'D' and resid 487 through 490' Processing helix chain 'D' and resid 506 through 508 No H-bonds generated for 'chain 'D' and resid 506 through 508' Processing helix chain 'D' and resid 526 through 528 No H-bonds generated for 'chain 'D' and resid 526 through 528' Processing helix chain 'D' and resid 549 through 557 Processing helix chain 'D' and resid 580 through 588 Processing helix chain 'D' and resid 615 through 624 Processing helix chain 'D' and resid 644 through 650 Processing helix chain 'D' and resid 668 through 676 removed outlier: 4.357A pdb=" N LEU D 676 " --> pdb=" O MET D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 703 Processing helix chain 'D' and resid 706 through 725 removed outlier: 3.955A pdb=" N ASP D 714 " --> pdb=" O ALA D 710 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS D 715 " --> pdb=" O GLN D 711 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR D 725 " --> pdb=" O PHE D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 762 removed outlier: 3.627A pdb=" N ARG D 752 " --> pdb=" O HIS D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 767 through 792 Processing helix chain 'D' and resid 798 through 804 removed outlier: 3.961A pdb=" N VAL D 803 " --> pdb=" O ILE D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 818 Processing helix chain 'D' and resid 846 through 850 Processing helix chain 'D' and resid 854 through 863 removed outlier: 3.719A pdb=" N LYS D 858 " --> pdb=" O HIS D 854 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY D 859 " --> pdb=" O GLY D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 867 through 880 Processing helix chain 'D' and resid 946 through 955 Processing helix chain 'D' and resid 965 through 967 No H-bonds generated for 'chain 'D' and resid 965 through 967' Processing helix chain 'D' and resid 976 through 979 No H-bonds generated for 'chain 'D' and resid 976 through 979' Processing helix chain 'D' and resid 995 through 1013 removed outlier: 3.691A pdb=" N ALA D 999 " --> pdb=" O VAL D 995 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA D1000 " --> pdb=" O GLY D 996 " (cutoff:3.500A) Proline residue: D1006 - end of helix removed outlier: 3.671A pdb=" N ARG D1013 " --> pdb=" O GLN D1009 " (cutoff:3.500A) Processing helix chain 'D' and resid 1024 through 1035 Proline residue: D1029 - end of helix Processing helix chain 'D' and resid 1118 through 1124 Processing helix chain 'D' and resid 1127 through 1145 removed outlier: 3.853A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR D1142 " --> pdb=" O VAL D1138 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1151 through 1161 removed outlier: 3.776A pdb=" N GLU D1155 " --> pdb=" O LYS D1152 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL D1156 " --> pdb=" O HIS D1153 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE D1157 " --> pdb=" O ILE D1154 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL D1158 " --> pdb=" O GLU D1155 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1194 Processing helix chain 'D' and resid 1220 through 1226 Processing helix chain 'D' and resid 1229 through 1239 Processing helix chain 'D' and resid 1248 through 1254 Processing helix chain 'D' and resid 1261 through 1263 No H-bonds generated for 'chain 'D' and resid 1261 through 1263' Processing helix chain 'D' and resid 1265 through 1268 No H-bonds generated for 'chain 'D' and resid 1265 through 1268' Processing helix chain 'D' and resid 1276 through 1281 Processing helix chain 'E' and resid 34 through 36 No H-bonds generated for 'chain 'E' and resid 34 through 36' Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.844A pdb=" N ASP E 45 " --> pdb=" O ASP E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 70 removed outlier: 4.164A pdb=" N VAL E 54 " --> pdb=" O LYS E 50 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN E 70 " --> pdb=" O ASP E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 101 Processing helix chain 'G' and resid 34 through 44 Processing helix chain 'G' and resid 59 through 73 Processing helix chain 'G' and resid 117 through 124 Processing helix chain 'G' and resid 144 through 149 Processing sheet with id= A, first strand: chain 'A' and resid 8 through 13 Processing sheet with id= B, first strand: chain 'A' and resid 85 through 87 Processing sheet with id= C, first strand: chain 'A' and resid 93 through 100 removed outlier: 4.079A pdb=" N SER A 53 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLU A 141 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N VAL A 51 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY A 143 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ALA A 49 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 103 through 106 Processing sheet with id= E, first strand: chain 'B' and resid 12 through 15 removed outlier: 6.573A pdb=" N ARG B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 93 through 100 removed outlier: 3.900A pdb=" N SER B 53 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU B 141 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N VAL B 51 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY B 143 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ALA B 49 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 103 through 106 Processing sheet with id= H, first strand: chain 'C' and resid 103 through 108 Processing sheet with id= I, first strand: chain 'C' and resid 130 through 132 Processing sheet with id= J, first strand: chain 'C' and resid 166 through 168 Processing sheet with id= K, first strand: chain 'C' and resid 178 through 181 Processing sheet with id= L, first strand: chain 'C' and resid 184 through 191 removed outlier: 4.297A pdb=" N HIS C 200 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU C 212 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU C 213 " --> pdb=" O ARG C 225 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 454 through 456 Processing sheet with id= N, first strand: chain 'C' and resid 528 through 531 Processing sheet with id= O, first strand: chain 'C' and resid 558 through 562 Processing sheet with id= P, first strand: chain 'C' and resid 667 through 671 removed outlier: 5.986A pdb=" N MET C 661 " --> pdb=" O ILE C 650 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ILE C 650 " --> pdb=" O MET C 661 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 1024 through 1031 removed outlier: 4.531A pdb=" N THR C1024 " --> pdb=" O ILE C 723 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE C 915 " --> pdb=" O ALA C 722 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 806 through 808 Processing sheet with id= S, first strand: chain 'C' and resid 884 through 886 removed outlier: 7.609A pdb=" N LEU C 737 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE C 898 " --> pdb=" O LEU C 737 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 748 through 760 removed outlier: 3.850A pdb=" N GLU C 867 " --> pdb=" O ALA C 759 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 93 through 96 Processing sheet with id= V, first strand: chain 'D' and resid 425 through 429 Processing sheet with id= W, first strand: chain 'D' and resid 430 through 432 removed outlier: 6.051A pdb=" N ILE D 522 " --> pdb=" O VAL D 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'D' and resid 633 through 637 Processing sheet with id= Y, first strand: chain 'D' and resid 897 through 899 Processing sheet with id= Z, first strand: chain 'D' and resid 1088 through 1090 Processing sheet with id= AA, first strand: chain 'D' and resid 1180 through 1182 removed outlier: 6.674A pdb=" N ALA D1202 " --> pdb=" O ILE D1168 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 135 through 139 removed outlier: 7.353A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 1061 through 1064 removed outlier: 3.959A pdb=" N ILE D1080 " --> pdb=" O TYR D1062 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE D1064 " --> pdb=" O ASP D1078 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ASP D1078 " --> pdb=" O ILE D1064 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 48 through 53 removed outlier: 3.719A pdb=" N GLN G 81 " --> pdb=" O ARG G 112 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 86 through 93 755 hydrogen bonds defined for protein. 2187 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 178 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 64 stacking parallelities Total time for adding SS restraints: 11.35 Time building geometry restraints manager: 11.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 4290 1.31 - 1.45: 6946 1.45 - 1.59: 14663 1.59 - 1.72: 173 1.72 - 1.86: 155 Bond restraints: 26227 Sorted by residual: bond pdb=" C2' 2TM C1201 " pdb=" C3' 2TM C1201 " ideal model delta sigma weight residual 1.511 1.296 0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C1' 2TM C1201 " pdb=" C2' 2TM C1201 " ideal model delta sigma weight residual 1.327 1.536 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C1' 2TM C1201 " pdb=" N1 2TM C1201 " ideal model delta sigma weight residual 1.432 1.339 0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C3' 2TM C1201 " pdb=" O3' 2TM C1201 " ideal model delta sigma weight residual 1.364 1.455 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C1' 2TM C1201 " pdb=" O4' 2TM C1201 " ideal model delta sigma weight residual 1.609 1.538 0.071 2.00e-02 2.50e+03 1.25e+01 ... (remaining 26222 not shown) Histogram of bond angle deviations from ideal: 98.83 - 105.86: 1062 105.86 - 112.90: 14253 112.90 - 119.94: 8974 119.94 - 126.97: 11160 126.97 - 134.01: 475 Bond angle restraints: 35924 Sorted by residual: angle pdb=" C GLU C1149 " pdb=" CA GLU C1149 " pdb=" CB GLU C1149 " ideal model delta sigma weight residual 115.89 109.99 5.90 1.32e+00 5.74e-01 1.99e+01 angle pdb=" C TYR D 61 " pdb=" N CYS D 62 " pdb=" CA CYS D 62 " ideal model delta sigma weight residual 121.71 117.22 4.49 1.39e+00 5.18e-01 1.04e+01 angle pdb=" C VAL D 476 " pdb=" CA VAL D 476 " pdb=" CB VAL D 476 " ideal model delta sigma weight residual 112.22 108.43 3.79 1.38e+00 5.25e-01 7.53e+00 angle pdb=" C ASN C 545 " pdb=" N SER C 546 " pdb=" CA SER C 546 " ideal model delta sigma weight residual 123.15 117.08 6.07 2.23e+00 2.01e-01 7.40e+00 angle pdb=" C VAL C 409 " pdb=" N GLU C 410 " pdb=" CA GLU C 410 " ideal model delta sigma weight residual 121.54 126.64 -5.10 1.91e+00 2.74e-01 7.12e+00 ... (remaining 35919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.49: 15217 33.49 - 66.98: 576 66.98 - 100.48: 10 100.48 - 133.97: 0 133.97 - 167.46: 1 Dihedral angle restraints: 15804 sinusoidal: 7027 harmonic: 8777 Sorted by residual: dihedral pdb=" O4' G R 20 " pdb=" C1' G R 20 " pdb=" N9 G R 20 " pdb=" C4 G R 20 " ideal model delta sinusoidal sigma weight residual 254.00 177.91 76.09 1 1.70e+01 3.46e-03 2.52e+01 dihedral pdb=" CA GLY D 63 " pdb=" C GLY D 63 " pdb=" N LYS D 64 " pdb=" CA LYS D 64 " ideal model delta harmonic sigma weight residual -180.00 -157.40 -22.60 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA SER A 44 " pdb=" C SER A 44 " pdb=" N SER A 45 " pdb=" CA SER A 45 " ideal model delta harmonic sigma weight residual 180.00 -158.90 -21.10 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 15801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2476 0.031 - 0.063: 1112 0.063 - 0.094: 315 0.094 - 0.125: 179 0.125 - 0.156: 16 Chirality restraints: 4098 Sorted by residual: chirality pdb=" CA ILE D1149 " pdb=" N ILE D1149 " pdb=" C ILE D1149 " pdb=" CB ILE D1149 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.10e-01 chirality pdb=" CA ILE D 509 " pdb=" N ILE D 509 " pdb=" C ILE D 509 " pdb=" CB ILE D 509 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" C3' 2TM C1201 " pdb=" C2' 2TM C1201 " pdb=" C4' 2TM C1201 " pdb=" O3' 2TM C1201 " both_signs ideal model delta sigma weight residual False -2.56 -2.41 -0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 4095 not shown) Planarity restraints: 4418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 576 " 0.041 5.00e-02 4.00e+02 6.28e-02 6.31e+00 pdb=" N PRO D 577 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 577 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 577 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 32 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.40e+00 pdb=" N PRO C 33 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 33 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 33 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 433 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO D 434 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 434 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 434 " -0.021 5.00e-02 4.00e+02 ... (remaining 4415 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 102 2.45 - 3.06: 17208 3.06 - 3.68: 35651 3.68 - 4.29: 53447 4.29 - 4.90: 92325 Nonbonded interactions: 198733 Sorted by model distance: nonbonded pdb=" O3G 2TM C1201 " pdb="MG MG D2002 " model vdw 1.840 2.170 nonbonded pdb=" OE2 GLU D1036 " pdb=" OG1 THR D1211 " model vdw 1.848 2.440 nonbonded pdb=" O1B 2TM C1201 " pdb="MG MG D2002 " model vdw 1.888 2.170 nonbonded pdb=" OG1 THR C 165 " pdb=" OE2 GLU C 172 " model vdw 1.964 2.440 nonbonded pdb=" NZ LYS D 123 " pdb=" OP2 DT N 36 " model vdw 1.970 2.520 ... (remaining 198728 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' and (resid 1 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 223 o \ r (resid 224 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 25 through 226)) selection = (chain 'B' and resid 1 through 226) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.220 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: 14.340 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 81.590 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 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 : 0.005 0.215 26227 Z= 0.317 Angle : 0.569 6.068 35924 Z= 0.324 Chirality : 0.042 0.156 4098 Planarity : 0.004 0.063 4418 Dihedral : 15.244 167.460 10164 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.18 % Favored : 94.66 % Rotamer: Outliers : 3.59 % Allowed : 8.54 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.15), residues: 3053 helix: 0.92 (0.17), residues: 1058 sheet: 0.29 (0.27), residues: 393 loop : -1.85 (0.14), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 778 HIS 0.005 0.001 HIS C 372 PHE 0.019 0.001 PHE C 906 TYR 0.012 0.001 TYR C 129 ARG 0.004 0.000 ARG D1163 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 188 time to evaluate : 3.008 Fit side-chains revert: symmetry clash revert: symmetry clash 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 303, in __init__ self.caller(self.optimize_sidechains) 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 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable