Starting phenix.real_space_refine (version: dev) on Tue Dec 20 14:29:31 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jl2_22370/12_2022/7jl2_22370_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jl2_22370/12_2022/7jl2_22370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jl2_22370/12_2022/7jl2_22370.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jl2_22370/12_2022/7jl2_22370.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jl2_22370/12_2022/7jl2_22370_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jl2_22370/12_2022/7jl2_22370_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 17661 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 370": "OE1" <-> "OE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 523": "OE1" <-> "OE2" Residue "A ASP 526": "OD1" <-> "OD2" Residue "A PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 572": "OD1" <-> "OD2" Residue "A TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 794": "OE1" <-> "OE2" Residue "A TYR 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 824": "NH1" <-> "NH2" Residue "A ASP 826": "OD1" <-> "OD2" Residue "A PHE 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 937": "OE1" <-> "OE2" Residue "A TYR 939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 991": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1015": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 336": "OD1" <-> "OD2" Residue "B PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 429": "OE1" <-> "OE2" Residue "B ASP 454": "OD1" <-> "OD2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 370": "OE1" <-> "OE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 523": "OE1" <-> "OE2" Residue "C ASP 526": "OD1" <-> "OD2" Residue "C PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 572": "OD1" <-> "OD2" Residue "C TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 794": "OE1" <-> "OE2" Residue "C TYR 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 824": "NH1" <-> "NH2" Residue "C ASP 826": "OD1" <-> "OD2" Residue "C PHE 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 937": "OE1" <-> "OE2" Residue "C TYR 939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 991": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1015": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 336": "OD1" <-> "OD2" Residue "D PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 454": "OD1" <-> "OD2" Residue "D PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 370": "OE1" <-> "OE2" Residue "E PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 523": "OE1" <-> "OE2" Residue "E ASP 526": "OD1" <-> "OD2" Residue "E PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 572": "OD1" <-> "OD2" Residue "E TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 794": "OE1" <-> "OE2" Residue "E TYR 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 824": "NH1" <-> "NH2" Residue "E ASP 826": "OD1" <-> "OD2" Residue "E PHE 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 937": "OE1" <-> "OE2" Residue "E TYR 939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 991": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1015": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 336": "OD1" <-> "OD2" Residue "F PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 429": "OE1" <-> "OE2" Residue "F ASP 454": "OD1" <-> "OD2" Residue "F PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 22128 Number of models: 1 Model: "" Number of chains: 11 Chain: "X" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 944 Classifications: {'RNA': 44} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 25, 'rna3p_pyr': 18} Link IDs: {'rna2p': 1, 'rna3p': 42} Chain: "Y" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 925 Classifications: {'RNA': 44} Modifications used: {'rna3p_pur': 18, 'rna3p_pyr': 26} Link IDs: {'rna3p': 43} Chain: "A" Number of atoms: 5311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5311 Classifications: {'peptide': 662} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 640} Chain breaks: 8 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 1408 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 180, 1398 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 167} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 48 Conformer: "B" Number of residues, atoms: 180, 1398 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 167} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 48 bond proxies already assigned to first conformer: 1432 Chain: "C" Number of atoms: 5311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5311 Classifications: {'peptide': 662} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 640} Chain breaks: 8 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 1408 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 180, 1398 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 167} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 48 Conformer: "B" Number of residues, atoms: 180, 1398 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 167} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 48 bond proxies already assigned to first conformer: 1432 Chain: "E" Number of atoms: 5311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5311 Classifications: {'peptide': 662} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 640} Chain breaks: 8 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 1408 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 180, 1398 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 167} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 48 Conformer: "B" Number of residues, atoms: 180, 1398 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 167} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 48 bond proxies already assigned to first conformer: 1432 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6372 SG CYS A 907 84.451 54.137 76.421 1.00181.77 S ATOM 6395 SG CYS A 910 86.208 51.144 75.913 1.00194.53 S ATOM 6728 SG CYS A 962 84.298 52.526 72.877 1.00190.33 S ATOM 6743 SG CYS A 964 82.507 50.685 75.575 1.00196.45 S ATOM 13091 SG CYS C 907 109.597 83.124 123.362 1.00191.35 S ATOM 13114 SG CYS C 910 112.674 84.733 122.867 1.00198.31 S ATOM 13447 SG CYS C 962 111.206 82.904 119.821 1.00189.02 S ATOM 13462 SG CYS C 964 112.950 81.014 122.515 1.00195.39 S ATOM 19810 SG CYS E 907 54.307 77.760 29.630 1.00180.73 S ATOM 19833 SG CYS E 910 51.411 75.846 29.129 1.00197.41 S ATOM 20166 SG CYS E 962 52.686 77.823 26.089 1.00201.33 S ATOM 20181 SG CYS E 964 50.757 79.518 28.787 1.00210.14 S Time building chain proxies: 15.56, per 1000 atoms: 0.70 Number of scatterers: 22128 At special positions: 0 Unit cell: (134.672, 165.75, 163.679, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 3 29.99 S 126 16.00 P 94 15.00 Al 3 13.00 Mg 3 11.99 F 12 9.00 O 4342 8.00 N 3854 7.00 C 13691 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: 10.23 Conformation dependent library (CDL) restraints added in 3.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 910 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 962 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 964 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 907 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 910 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 962 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 964 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 907 " pdb=" ZN E1101 " pdb="ZN ZN E1101 " - pdb=" SG CYS E 910 " pdb="ZN ZN E1101 " - pdb=" SG CYS E 962 " pdb="ZN ZN E1101 " - pdb=" SG CYS E 964 " pdb="ZN ZN E1101 " - pdb=" SG CYS E 907 " Number of angles added : 18 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4806 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 87 helices and 24 sheets defined 39.3% alpha, 15.1% beta 28 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 8.07 Creating SS restraints... Processing helix chain 'A' and resid 310 through 316 Processing helix chain 'A' and resid 318 through 320 No H-bonds generated for 'chain 'A' and resid 318 through 320' Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 366 through 376 removed outlier: 3.861A pdb=" N GLU A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 381 No H-bonds generated for 'chain 'A' and resid 378 through 381' Processing helix chain 'A' and resid 400 through 406 Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 434 through 436 No H-bonds generated for 'chain 'A' and resid 434 through 436' Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 453 through 472 removed outlier: 3.721A pdb=" N ILE A 457 " --> pdb=" O VAL A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 513 Processing helix chain 'A' and resid 525 through 531 Processing helix chain 'A' and resid 549 through 564 Processing helix chain 'A' and resid 576 through 592 Processing helix chain 'A' and resid 598 through 616 Processing helix chain 'A' and resid 619 through 639 removed outlier: 3.594A pdb=" N ALA A 639 " --> pdb=" O ASP A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 691 removed outlier: 4.551A pdb=" N LEU A 679 " --> pdb=" O PHE A 675 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU A 682 " --> pdb=" O THR A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 715 Processing helix chain 'A' and resid 728 through 740 Processing helix chain 'A' and resid 742 through 747 removed outlier: 4.101A pdb=" N VAL A 747 " --> pdb=" O LYS A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 780 Processing helix chain 'A' and resid 790 through 792 No H-bonds generated for 'chain 'A' and resid 790 through 792' Processing helix chain 'A' and resid 814 through 822 removed outlier: 4.151A pdb=" N ALA A 819 " --> pdb=" O ALA A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 863 removed outlier: 3.719A pdb=" N ASN A 863 " --> pdb=" O HIS A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 894 removed outlier: 3.532A pdb=" N ILE A 881 " --> pdb=" O GLN A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 919 No H-bonds generated for 'chain 'A' and resid 917 through 919' Processing helix chain 'A' and resid 933 through 938 Processing helix chain 'A' and resid 984 through 986 No H-bonds generated for 'chain 'A' and resid 984 through 986' Processing helix chain 'B' and resid 322 through 329 removed outlier: 4.149A pdb=" N GLN B 328 " --> pdb=" O ARG B 324 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ASN B 329 " --> pdb=" O LYS B 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 316 Processing helix chain 'C' and resid 318 through 320 No H-bonds generated for 'chain 'C' and resid 318 through 320' Processing helix chain 'C' and resid 335 through 353 Processing helix chain 'C' and resid 366 through 376 removed outlier: 3.862A pdb=" N GLU C 370 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU C 376 " --> pdb=" O LEU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 381 No H-bonds generated for 'chain 'C' and resid 378 through 381' Processing helix chain 'C' and resid 400 through 406 Processing helix chain 'C' and resid 414 through 421 Processing helix chain 'C' and resid 434 through 436 No H-bonds generated for 'chain 'C' and resid 434 through 436' Processing helix chain 'C' and resid 445 through 447 No H-bonds generated for 'chain 'C' and resid 445 through 447' Processing helix chain 'C' and resid 453 through 472 removed outlier: 3.722A pdb=" N ILE C 457 " --> pdb=" O VAL C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 513 Processing helix chain 'C' and resid 525 through 531 Processing helix chain 'C' and resid 549 through 564 Processing helix chain 'C' and resid 576 through 592 Processing helix chain 'C' and resid 598 through 616 Processing helix chain 'C' and resid 619 through 639 removed outlier: 3.594A pdb=" N ALA C 639 " --> pdb=" O ASP C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 691 removed outlier: 4.552A pdb=" N LEU C 679 " --> pdb=" O PHE C 675 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU C 682 " --> pdb=" O THR C 678 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 715 Processing helix chain 'C' and resid 728 through 740 Processing helix chain 'C' and resid 742 through 747 removed outlier: 4.101A pdb=" N VAL C 747 " --> pdb=" O LYS C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 780 Processing helix chain 'C' and resid 790 through 792 No H-bonds generated for 'chain 'C' and resid 790 through 792' Processing helix chain 'C' and resid 814 through 822 removed outlier: 4.151A pdb=" N ALA C 819 " --> pdb=" O ALA C 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 863 removed outlier: 3.718A pdb=" N ASN C 863 " --> pdb=" O HIS C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 894 removed outlier: 3.533A pdb=" N ILE C 881 " --> pdb=" O GLN C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 919 No H-bonds generated for 'chain 'C' and resid 917 through 919' Processing helix chain 'C' and resid 933 through 938 Processing helix chain 'C' and resid 984 through 986 No H-bonds generated for 'chain 'C' and resid 984 through 986' Processing helix chain 'D' and resid 322 through 329 removed outlier: 4.297A pdb=" N GLN D 328 " --> pdb=" O ARG D 324 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ASN D 329 " --> pdb=" O LYS D 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 316 Processing helix chain 'E' and resid 318 through 320 No H-bonds generated for 'chain 'E' and resid 318 through 320' Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 366 through 376 removed outlier: 3.861A pdb=" N GLU E 370 " --> pdb=" O VAL E 366 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU E 376 " --> pdb=" O LEU E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 381 No H-bonds generated for 'chain 'E' and resid 378 through 381' Processing helix chain 'E' and resid 400 through 406 Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 434 through 436 No H-bonds generated for 'chain 'E' and resid 434 through 436' Processing helix chain 'E' and resid 445 through 447 No H-bonds generated for 'chain 'E' and resid 445 through 447' Processing helix chain 'E' and resid 453 through 472 removed outlier: 3.721A pdb=" N ILE E 457 " --> pdb=" O VAL E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 513 Processing helix chain 'E' and resid 525 through 531 Processing helix chain 'E' and resid 549 through 564 Processing helix chain 'E' and resid 576 through 592 Processing helix chain 'E' and resid 598 through 616 Processing helix chain 'E' and resid 619 through 639 removed outlier: 3.595A pdb=" N ALA E 639 " --> pdb=" O ASP E 635 " (cutoff:3.500A) Processing helix chain 'E' and resid 674 through 691 removed outlier: 4.552A pdb=" N LEU E 679 " --> pdb=" O PHE E 675 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU E 682 " --> pdb=" O THR E 678 " (cutoff:3.500A) Processing helix chain 'E' and resid 699 through 715 Processing helix chain 'E' and resid 728 through 740 Processing helix chain 'E' and resid 742 through 747 removed outlier: 4.100A pdb=" N VAL E 747 " --> pdb=" O LYS E 743 " (cutoff:3.500A) Processing helix chain 'E' and resid 768 through 780 Processing helix chain 'E' and resid 790 through 792 No H-bonds generated for 'chain 'E' and resid 790 through 792' Processing helix chain 'E' and resid 814 through 822 removed outlier: 4.151A pdb=" N ALA E 819 " --> pdb=" O ALA E 815 " (cutoff:3.500A) Processing helix chain 'E' and resid 841 through 863 removed outlier: 3.719A pdb=" N ASN E 863 " --> pdb=" O HIS E 859 " (cutoff:3.500A) Processing helix chain 'E' and resid 866 through 894 removed outlier: 3.532A pdb=" N ILE E 881 " --> pdb=" O GLN E 877 " (cutoff:3.500A) Processing helix chain 'E' and resid 917 through 919 No H-bonds generated for 'chain 'E' and resid 917 through 919' Processing helix chain 'E' and resid 933 through 938 Processing helix chain 'E' and resid 984 through 986 No H-bonds generated for 'chain 'E' and resid 984 through 986' Processing helix chain 'F' and resid 322 through 329 removed outlier: 4.315A pdb=" N GLN F 328 " --> pdb=" O ARG F 324 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ASN F 329 " --> pdb=" O LYS F 325 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.755A pdb=" N GLY A 486 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 536 through 542 Processing sheet with id= C, first strand: chain 'A' and resid 987 through 990 removed outlier: 3.686A pdb=" N CYS A 915 " --> pdb=" O PHE A 905 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N CYS A 907 " --> pdb=" O LEU A 913 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU A 913 " --> pdb=" O CYS A 907 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 920 through 923 Processing sheet with id= E, first strand: chain 'A' and resid 940 through 942 Processing sheet with id= F, first strand: chain 'A' and resid 971 through 974 Processing sheet with id= G, first strand: chain 'B' and resid 344 through 347 removed outlier: 3.556A pdb=" N TYR B 475 " --> pdb=" O PHE B 464 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N SER B 466 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 372 through 374 Processing sheet with id= I, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.754A pdb=" N GLY C 486 " --> pdb=" O ILE C 325 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 536 through 542 Processing sheet with id= K, first strand: chain 'C' and resid 987 through 990 removed outlier: 3.685A pdb=" N CYS C 915 " --> pdb=" O PHE C 905 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N CYS C 907 " --> pdb=" O LEU C 913 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU C 913 " --> pdb=" O CYS C 907 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 920 through 923 Processing sheet with id= M, first strand: chain 'C' and resid 940 through 942 Processing sheet with id= N, first strand: chain 'C' and resid 971 through 974 Processing sheet with id= O, first strand: chain 'D' and resid 344 through 347 removed outlier: 3.730A pdb=" N TRP D 386 " --> pdb=" O MET D 453 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET D 453 " --> pdb=" O TRP D 386 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR D 475 " --> pdb=" O PHE D 464 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N SER D 466 " --> pdb=" O PRO D 473 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 372 through 374 Processing sheet with id= Q, first strand: chain 'E' and resid 325 through 328 removed outlier: 3.754A pdb=" N GLY E 486 " --> pdb=" O ILE E 325 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 536 through 542 Processing sheet with id= S, first strand: chain 'E' and resid 987 through 990 removed outlier: 3.686A pdb=" N CYS E 915 " --> pdb=" O PHE E 905 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N CYS E 907 " --> pdb=" O LEU E 913 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU E 913 " --> pdb=" O CYS E 907 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 920 through 923 Processing sheet with id= U, first strand: chain 'E' and resid 940 through 942 Processing sheet with id= V, first strand: chain 'E' and resid 971 through 974 Processing sheet with id= W, first strand: chain 'F' and resid 344 through 347 removed outlier: 3.680A pdb=" N TRP F 386 " --> pdb=" O MET F 453 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET F 453 " --> pdb=" O TRP F 386 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR F 475 " --> pdb=" O PHE F 464 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N SER F 466 " --> pdb=" O PRO F 473 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 372 through 374 914 hydrogen bonds defined for protein. 2637 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 71 hydrogen bonds 142 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 8.80 Time building geometry restraints manager: 11.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6190 1.33 - 1.46: 4853 1.46 - 1.58: 11300 1.58 - 1.70: 186 1.70 - 1.82: 207 Bond restraints: 22736 Sorted by residual: bond pdb=" CA LYS A 782 " pdb=" C LYS A 782 " ideal model delta sigma weight residual 1.523 1.599 -0.076 1.48e-02 4.57e+03 2.64e+01 bond pdb=" CA LYS E 782 " pdb=" C LYS E 782 " ideal model delta sigma weight residual 1.523 1.599 -0.076 1.48e-02 4.57e+03 2.62e+01 bond pdb=" CA LYS C 782 " pdb=" C LYS C 782 " ideal model delta sigma weight residual 1.523 1.599 -0.076 1.48e-02 4.57e+03 2.62e+01 bond pdb=" F1 ALF E1103 " pdb="AL ALF E1103 " ideal model delta sigma weight residual 1.684 1.781 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" F1 ALF C1103 " pdb="AL ALF C1103 " ideal model delta sigma weight residual 1.684 1.781 -0.097 2.00e-02 2.50e+03 2.34e+01 ... (remaining 22731 not shown) Histogram of bond angle deviations from ideal: 89.52 - 107.52: 1428 107.52 - 125.52: 29087 125.52 - 143.53: 604 143.53 - 161.53: 0 161.53 - 179.53: 6 Bond angle restraints: 31125 Sorted by residual: angle pdb=" F1 ALF E1103 " pdb="AL ALF E1103 " pdb=" F2 ALF E1103 " ideal model delta sigma weight residual 108.68 179.46 -70.78 3.00e+00 1.11e-01 5.57e+02 angle pdb=" F1 ALF A1103 " pdb="AL ALF A1103 " pdb=" F2 ALF A1103 " ideal model delta sigma weight residual 108.68 179.44 -70.76 3.00e+00 1.11e-01 5.56e+02 angle pdb=" F1 ALF C1103 " pdb="AL ALF C1103 " pdb=" F2 ALF C1103 " ideal model delta sigma weight residual 108.68 179.42 -70.74 3.00e+00 1.11e-01 5.56e+02 angle pdb=" F3 ALF C1103 " pdb="AL ALF C1103 " pdb=" F4 ALF C1103 " ideal model delta sigma weight residual 109.63 179.53 -69.90 3.00e+00 1.11e-01 5.43e+02 angle pdb=" F3 ALF A1103 " pdb="AL ALF A1103 " pdb=" F4 ALF A1103 " ideal model delta sigma weight residual 109.63 179.52 -69.89 3.00e+00 1.11e-01 5.43e+02 ... (remaining 31120 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.56: 13345 34.56 - 69.13: 244 69.13 - 103.69: 30 103.69 - 138.25: 3 138.25 - 172.82: 4 Dihedral angle restraints: 13626 sinusoidal: 6237 harmonic: 7389 Sorted by residual: dihedral pdb=" C5' ADP A1102 " pdb=" O5' ADP A1102 " pdb=" PA ADP A1102 " pdb=" O2A ADP A1102 " ideal model delta sinusoidal sigma weight residual -60.00 83.47 -143.47 1 2.00e+01 2.50e-03 4.33e+01 dihedral pdb=" C5' ADP E1102 " pdb=" O5' ADP E1102 " pdb=" PA ADP E1102 " pdb=" O2A ADP E1102 " ideal model delta sinusoidal sigma weight residual -60.00 83.43 -143.43 1 2.00e+01 2.50e-03 4.33e+01 dihedral pdb=" C5' ADP C1102 " pdb=" O5' ADP C1102 " pdb=" PA ADP C1102 " pdb=" O2A ADP C1102 " ideal model delta sinusoidal sigma weight residual -60.00 83.40 -143.40 1 2.00e+01 2.50e-03 4.33e+01 ... (remaining 13623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3110 0.066 - 0.132: 416 0.132 - 0.198: 19 0.198 - 0.265: 3 0.265 - 0.331: 3 Chirality restraints: 3551 Sorted by residual: chirality pdb=" CA LYS A 782 " pdb=" N LYS A 782 " pdb=" C LYS A 782 " pdb=" CB LYS A 782 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CA LYS E 782 " pdb=" N LYS E 782 " pdb=" C LYS E 782 " pdb=" CB LYS E 782 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CA LYS C 782 " pdb=" N LYS C 782 " pdb=" C LYS C 782 " pdb=" CB LYS C 782 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 3548 not shown) Planarity restraints: 3631 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A X 15 " 0.042 2.00e-02 2.50e+03 1.88e-02 9.73e+00 pdb=" N9 A X 15 " -0.043 2.00e-02 2.50e+03 pdb=" C8 A X 15 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A X 15 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A X 15 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A X 15 " 0.006 2.00e-02 2.50e+03 pdb=" N6 A X 15 " 0.010 2.00e-02 2.50e+03 pdb=" N1 A X 15 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A X 15 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A X 15 " -0.007 2.00e-02 2.50e+03 pdb=" C4 A X 15 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 790 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.91e+00 pdb=" C THR A 790 " 0.034 2.00e-02 2.50e+03 pdb=" O THR A 790 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL A 791 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 790 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C THR C 790 " 0.034 2.00e-02 2.50e+03 pdb=" O THR C 790 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL C 791 " -0.011 2.00e-02 2.50e+03 ... (remaining 3628 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 209 2.49 - 3.09: 16865 3.09 - 3.70: 35244 3.70 - 4.30: 48625 4.30 - 4.90: 75117 Nonbonded interactions: 176060 Sorted by model distance: nonbonded pdb=" F4 ALF C1103 " pdb="MG MG C1104 " model vdw 1.889 2.120 nonbonded pdb=" F4 ALF E1103 " pdb="MG MG E1104 " model vdw 1.889 2.120 nonbonded pdb=" F4 ALF A1103 " pdb="MG MG A1104 " model vdw 1.889 2.120 nonbonded pdb=" F1 ALF E1103 " pdb="MG MG E1104 " model vdw 1.891 2.120 nonbonded pdb=" F1 ALF A1103 " pdb="MG MG A1104 " model vdw 1.892 2.120 ... (remaining 176055 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 'C' selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 321 through 387 or resid 389 through 432 or resid 434 thro \ ugh 502)) selection = (chain 'D' and (resid 321 through 387 or resid 389 through 432 or resid 434 thro \ ugh 502)) selection = (chain 'F' and (resid 321 through 387 or resid 389 through 432 or resid 434 thro \ ugh 502)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians Zn 3 6.06 5 Al 3 5.89 5 P 94 5.49 5 Mg 3 5.21 5 S 126 5.16 5 C 13691 2.51 5 N 3854 2.21 5 O 4342 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.290 Construct map_model_manager: 0.020 Extract box with map and model: 5.430 Check model and map are aligned: 0.390 Convert atoms to be neutral: 0.200 Process input model: 74.180 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.097 22736 Z= 0.412 Angle : 1.348 70.785 31125 Z= 0.577 Chirality : 0.045 0.331 3551 Planarity : 0.004 0.034 3631 Dihedral : 14.410 172.817 8820 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 3.03 % 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: -0.56 (0.17), residues: 2466 helix: 0.45 (0.16), residues: 927 sheet: 0.18 (0.23), residues: 501 loop : -1.38 (0.20), residues: 1038 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 200 time to evaluate : 2.624 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 208 average time/residue: 0.3144 time to fit residues: 103.9731 Evaluate side-chains 147 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 141 time to evaluate : 2.440 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2360 time to fit residues: 5.8036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 1.9990 chunk 197 optimal weight: 0.0670 chunk 109 optimal weight: 6.9990 chunk 67 optimal weight: 20.0000 chunk 132 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 203 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 151 optimal weight: 8.9990 chunk 236 optimal weight: 9.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 835 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 HIS ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 ASN ** C 835 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 835 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 22736 Z= 0.150 Angle : 0.568 6.305 31125 Z= 0.290 Chirality : 0.041 0.143 3551 Planarity : 0.003 0.028 3631 Dihedral : 8.443 173.686 3774 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.38 (0.17), residues: 2466 helix: 1.64 (0.17), residues: 939 sheet: 0.41 (0.24), residues: 483 loop : -1.12 (0.20), residues: 1044 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 2.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.3079 time to fit residues: 118.6106 Evaluate side-chains 157 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 2.581 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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-4807/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-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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: 50.3026 > 50: distance: 89 - 94: 6.389 distance: 94 - 95: 3.028 distance: 95 - 98: 3.874 distance: 96 - 97: 23.245 distance: 96 - 103: 15.210 distance: 98 - 99: 4.944 distance: 99 - 100: 11.567 distance: 100 - 101: 7.912 distance: 100 - 102: 7.554 distance: 103 - 104: 11.469 distance: 104 - 105: 9.804 distance: 104 - 107: 9.794 distance: 105 - 106: 12.332 distance: 105 - 111: 18.070 distance: 107 - 108: 7.100 distance: 108 - 109: 3.784 distance: 108 - 110: 5.309 distance: 111 - 112: 19.641 distance: 111 - 117: 11.923 distance: 112 - 113: 16.828 distance: 112 - 115: 12.329 distance: 113 - 114: 28.187 distance: 113 - 118: 12.749 distance: 115 - 116: 16.615 distance: 116 - 117: 13.156 distance: 118 - 119: 14.835 distance: 119 - 120: 14.511 distance: 119 - 122: 10.581 distance: 120 - 121: 32.604 distance: 120 - 126: 7.866 distance: 122 - 123: 17.732 distance: 122 - 124: 21.628 distance: 123 - 125: 12.642 distance: 126 - 127: 7.053 distance: 127 - 128: 4.563 distance: 127 - 130: 12.693 distance: 128 - 129: 14.606 distance: 128 - 133: 20.438 distance: 130 - 131: 15.456 distance: 130 - 132: 17.452 distance: 133 - 134: 8.974 distance: 134 - 135: 9.129 distance: 134 - 137: 9.400 distance: 135 - 136: 30.150 distance: 135 - 144: 8.984 distance: 137 - 138: 15.900 distance: 138 - 139: 5.925 distance: 138 - 140: 7.097 distance: 139 - 141: 7.460 distance: 140 - 142: 10.383 distance: 142 - 143: 11.342 distance: 144 - 145: 5.857 distance: 144 - 150: 15.835 distance: 145 - 146: 5.171 distance: 145 - 148: 12.592 distance: 146 - 147: 13.582 distance: 146 - 151: 4.431 distance: 148 - 149: 11.002 distance: 149 - 150: 13.287 distance: 151 - 152: 5.750 distance: 152 - 155: 6.015 distance: 153 - 154: 4.474 distance: 153 - 159: 4.083 distance: 155 - 156: 4.931 distance: 156 - 157: 3.411 distance: 156 - 158: 5.013 distance: 159 - 160: 4.382 distance: 160 - 161: 5.737 distance: 161 - 162: 5.957 distance: 163 - 164: 3.192 distance: 164 - 165: 14.118 distance: 164 - 166: 6.451 distance: 167 - 168: 3.770 distance: 168 - 169: 5.077 distance: 168 - 171: 10.519 distance: 169 - 170: 19.724 distance: 169 - 175: 10.911 distance: 171 - 172: 6.576 distance: 172 - 173: 4.460 distance: 172 - 174: 3.657