Starting phenix.real_space_refine on Sat Aug 23 19:14:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8off_16859/08_2025/8off_16859.cif Found real_map, /net/cci-nas-00/data/ceres_data/8off_16859/08_2025/8off_16859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8off_16859/08_2025/8off_16859.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8off_16859/08_2025/8off_16859.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8off_16859/08_2025/8off_16859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8off_16859/08_2025/8off_16859.map" } resolution = 3.4 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 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= 0.008 sd= 0.081 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: 5 Type Number sf(0) Gaussians P 289 5.49 5 S 20 5.16 5 C 8204 2.51 5 N 2691 2.21 5 O 3220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14424 Number of models: 1 Model: "" Number of chains: 13 Chain: "J" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2938 Classifications: {'DNA': 144} Link IDs: {'rna3p': 143} Chain: "Ca" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 779 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 92} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Ba" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 701 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 89} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Aa" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 774 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 100} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "Bb" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 709 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Da" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 611 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 75} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Ab" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 778 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "Cb" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 774 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "Db" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 662 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "Ea" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 822 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 115} Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'ASP:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 62 Chain: "Fa" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 525 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 48 Chain: "Eb" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 199, 1361 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 9, 'TRANS': 189} Chain breaks: 1 Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 176 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLU:plan': 12, 'GLN:plan1': 5, 'ASP:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 98 Conformer: "B" Number of residues, atoms: 199, 1361 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 9, 'TRANS': 189} Chain breaks: 1 Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 176 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLU:plan': 12, 'GLN:plan1': 5, 'ASP:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 98 bond proxies already assigned to first conformer: 1391 Chain: "I" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2988 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Time building chain proxies: 3.24, per 1000 atoms: 0.22 Number of scatterers: 14424 At special positions: 0 Unit cell: (105.78, 129, 122.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 289 15.00 O 3220 8.00 N 2691 7.00 C 8204 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 - 3.00 Amino acid : True - 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: 1.01 Conformation dependent library (CDL) restraints added in 456.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2146 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 9 sheets defined 58.4% alpha, 3.6% beta 31 base pairs and 207 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'Ca' and resid 45 through 56 removed outlier: 4.097A pdb=" N LEUCa 49 " --> pdb=" O GLYCa 45 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 64 through 80 removed outlier: 3.804A pdb=" N PHECa 68 " --> pdb=" O ARGCa 64 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 87 through 114 removed outlier: 4.027A pdb=" N METCa 91 " --> pdb=" O SERCa 87 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEUCa 101 " --> pdb=" O CYSCa 97 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASPCa 107 " --> pdb=" O GLYCa 103 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 123 through 133 Processing helix chain 'Ba' and resid 40 through 50 removed outlier: 3.591A pdb=" N LYSBa 44 " --> pdb=" O VALBa 40 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 56 through 58 No H-bonds generated for 'chain 'Ba' and resid 56 through 58' Processing helix chain 'Ba' and resid 59 through 84 removed outlier: 3.961A pdb=" N METBa 63 " --> pdb=" O ALABa 59 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 91 through 103 removed outlier: 3.758A pdb=" N ILEBa 95 " --> pdb=" O THRBa 91 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 104 through 125 removed outlier: 3.576A pdb=" N ALABa 108 " --> pdb=" O PROBa 104 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYSBa 109 " --> pdb=" O GLYBa 105 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N HISBa 110 " --> pdb=" O GLUBa 106 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SERBa 125 " --> pdb=" O LYSBa 121 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 28 through 37 Processing helix chain 'Aa' and resid 48 through 73 removed outlier: 3.744A pdb=" N LEUAa 52 " --> pdb=" O ALAAa 48 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALAAa 54 " --> pdb=" O VALAa 50 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALAAa 70 " --> pdb=" O LEUAa 66 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 80 through 89 removed outlier: 3.856A pdb=" N LEUAa 84 " --> pdb=" O ILEAa 80 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 41 through 50 removed outlier: 3.878A pdb=" N VALBb 45 " --> pdb=" O TYRBb 41 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 57 through 85 removed outlier: 3.811A pdb=" N VALBb 67 " --> pdb=" O METBb 63 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASNBb 68 " --> pdb=" O ASNBb 64 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILEBb 70 " --> pdb=" O PHEBb 66 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARGBb 80 " --> pdb=" O GLYBb 76 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASNBb 85 " --> pdb=" O LEUBb 81 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 91 through 102 removed outlier: 3.599A pdb=" N ILEBb 95 " --> pdb=" O THRBb 91 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 104 through 106 No H-bonds generated for 'chain 'Bb' and resid 104 through 106' Processing helix chain 'Bb' and resid 107 through 124 removed outlier: 4.303A pdb=" N SERBb 113 " --> pdb=" O LYSBb 109 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SERBb 124 " --> pdb=" O THRBb 120 " (cutoff:3.500A) Processing helix chain 'Da' and resid 26 through 30 Processing helix chain 'Da' and resid 31 through 43 removed outlier: 3.748A pdb=" N ILEDa 35 " --> pdb=" O THRDa 31 " (cutoff:3.500A) Processing helix chain 'Da' and resid 51 through 77 removed outlier: 3.989A pdb=" N ALADa 77 " --> pdb=" O TYRDa 73 " (cutoff:3.500A) Processing helix chain 'Da' and resid 83 through 93 removed outlier: 3.757A pdb=" N VALDa 87 " --> pdb=" O THRDa 83 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 17 through 22 removed outlier: 3.587A pdb=" N ARGAb 21 " --> pdb=" O THRAb 17 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALAAb 22 " --> pdb=" O ARGAb 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ab' and resid 17 through 22' Processing helix chain 'Ab' and resid 28 through 37 Processing helix chain 'Ab' and resid 47 through 74 removed outlier: 3.819A pdb=" N TYRAb 51 " --> pdb=" O GLYAb 47 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEUAb 66 " --> pdb=" O GLUAb 62 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLYAb 68 " --> pdb=" O LEUAb 64 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASNAb 69 " --> pdb=" O GLUAb 65 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALAAb 70 " --> pdb=" O LEUAb 66 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASNAb 74 " --> pdb=" O ALAAb 70 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 80 through 90 removed outlier: 3.772A pdb=" N LEUAb 84 " --> pdb=" O ILEAb 80 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 93 through 98 removed outlier: 3.709A pdb=" N LEUAb 97 " --> pdb=" O GLUAb 93 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEUAb 98 " --> pdb=" O LEUAb 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ab' and resid 93 through 98' Processing helix chain 'Cb' and resid 46 through 56 Processing helix chain 'Cb' and resid 65 through 77 removed outlier: 3.504A pdb=" N GLNCb 69 " --> pdb=" O LYSCb 65 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 86 through 115 removed outlier: 4.382A pdb=" N VALCb 90 " --> pdb=" O GLNCb 86 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALACb 115 " --> pdb=" O CYSCb 111 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 121 through 133 removed outlier: 3.800A pdb=" N ILECb 125 " --> pdb=" O METCb 121 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLYCb 133 " --> pdb=" O ARGCb 129 " (cutoff:3.500A) Processing helix chain 'Db' and resid 26 through 30 removed outlier: 3.558A pdb=" N GLYDb 29 " --> pdb=" O ASNDb 26 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILEDb 30 " --> pdb=" O ILEDb 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'Db' and resid 26 through 30' Processing helix chain 'Db' and resid 31 through 43 removed outlier: 3.692A pdb=" N ILEDb 35 " --> pdb=" O THRDb 31 " (cutoff:3.500A) Processing helix chain 'Db' and resid 50 through 77 removed outlier: 4.446A pdb=" N GLUDb 54 " --> pdb=" O LEUDb 50 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASPDb 69 " --> pdb=" O ASNDb 65 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALADb 77 " --> pdb=" O TYRDb 73 " (cutoff:3.500A) Processing helix chain 'Db' and resid 83 through 95 removed outlier: 4.021A pdb=" N VALDb 87 " --> pdb=" O THRDb 83 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VALDb 88 " --> pdb=" O ALADb 84 " (cutoff:3.500A) Processing helix chain 'Ea' and resid 426 through 434 removed outlier: 3.818A pdb=" N LYSEa 434 " --> pdb=" O ILEEa 430 " (cutoff:3.500A) Processing helix chain 'Ea' and resid 436 through 447 Processing helix chain 'Ea' and resid 459 through 468 Processing helix chain 'Ea' and resid 469 through 478 removed outlier: 3.730A pdb=" N VALEa 473 " --> pdb=" O HISEa 469 " (cutoff:3.500A) Processing helix chain 'Ea' and resid 492 through 501 removed outlier: 3.608A pdb=" N ASPEa 496 " --> pdb=" O SEREa 492 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLYEa 501 " --> pdb=" O ALAEa 497 " (cutoff:3.500A) Processing helix chain 'Ea' and resid 503 through 513 removed outlier: 3.549A pdb=" N LYSEa 507 " --> pdb=" O METEa 503 " (cutoff:3.500A) Processing helix chain 'Ea' and resid 525 through 530 removed outlier: 3.887A pdb=" N ALAEa 530 " --> pdb=" O VALEa 527 " (cutoff:3.500A) Processing helix chain 'Ea' and resid 532 through 537 Processing helix chain 'Fa' and resid 22 through 32 Processing helix chain 'Fa' and resid 55 through 60 Processing helix chain 'Eb' and resid 574 through 589 Processing helix chain 'Eb' and resid 613 through 623 Processing helix chain 'Eb' and resid 628 through 639 removed outlier: 3.810A pdb=" N VALEb 632 " --> pdb=" O LYSEb 628 " (cutoff:3.500A) Processing helix chain 'Eb' and resid 654 through 661 Processing helix chain 'Eb' and resid 684 through 695 Processing helix chain 'Eb' and resid 707 through 712 Processing helix chain 'Eb' and resid 756 through 764 removed outlier: 3.739A pdb=" N METEb 764 " --> pdb=" O ILEEb 760 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Ca' and resid 84 through 85 removed outlier: 7.148A pdb=" N ARGCa 84 " --> pdb=" O VALDb 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'Ca' and resid 119 through 120 removed outlier: 3.506A pdb=" N ILECa 120 " --> pdb=" O ARGDb 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'Ba' and resid 89 through 90 Processing sheet with id=AA4, first strand: chain 'Aa' and resid 101 through 103 removed outlier: 6.770A pdb=" N THRAa 102 " --> pdb=" O TYRDb 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'Da' and resid 46 through 47 removed outlier: 7.629A pdb=" N ARGDa 46 " --> pdb=" O ILECb 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'Da' and resid 81 through 82 Processing sheet with id=AA7, first strand: chain 'Fa' and resid 11 through 16 removed outlier: 3.806A pdb=" N LYSFa 11 " --> pdb=" O THRFa 7 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N LEUFa 67 " --> pdb=" O GLNFa 2 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N PHEFa 4 " --> pdb=" O LEUFa 67 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEUFa 69 " --> pdb=" O PHEFa 4 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LYSFa 6 " --> pdb=" O LEUFa 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Eb' and resid 603 through 604 removed outlier: 6.570A pdb=" N VALEb 603 " --> pdb=" O LEUEb 627 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'Eb' and resid 697 through 698 removed outlier: 6.645A pdb=" N TYREb 672 " --> pdb=" O TYREb 732 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILEEb 734 " --> pdb=" O TYREb 672 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYREb 674 " --> pdb=" O ILEEb 734 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ALAEb 754 " --> pdb=" O GLNEb 731 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILEEb 733 " --> pdb=" O ALAEb 754 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 86 hydrogen bonds 172 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 207 stacking parallelities Total time for adding SS restraints: 2.18 Time building geometry restraints manager: 1.29 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: 2704 1.33 - 1.45: 4800 1.45 - 1.57: 7174 1.57 - 1.69: 575 1.69 - 1.81: 31 Bond restraints: 15284 Sorted by residual: bond pdb=" O3' DT I -67 " pdb=" P DG I -66 " ideal model delta sigma weight residual 1.607 1.548 0.059 1.50e-02 4.44e+03 1.56e+01 bond pdb=" O3' DG I -66 " pdb=" P DT I -65 " ideal model delta sigma weight residual 1.607 1.583 0.024 1.50e-02 4.44e+03 2.65e+00 bond pdb=" CA ILEDb 30 " pdb=" CB ILEDb 30 " ideal model delta sigma weight residual 1.540 1.520 0.020 1.36e-02 5.41e+03 2.20e+00 bond pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " ideal model delta sigma weight residual 1.422 1.466 -0.044 3.00e-02 1.11e+03 2.18e+00 bond pdb=" C HISBa 50 " pdb=" O HISBa 50 " ideal model delta sigma weight residual 1.249 1.237 0.012 8.50e-03 1.38e+04 2.08e+00 ... (remaining 15279 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 20743 1.29 - 2.57: 1098 2.57 - 3.86: 109 3.86 - 5.14: 18 5.14 - 6.43: 7 Bond angle restraints: 21975 Sorted by residual: angle pdb=" N VALAb 115 " pdb=" CA VALAb 115 " pdb=" C VALAb 115 " ideal model delta sigma weight residual 111.88 107.03 4.85 1.06e+00 8.90e-01 2.09e+01 angle pdb=" O3' DG I -66 " pdb=" C3' DG I -66 " pdb=" C2' DG I -66 " ideal model delta sigma weight residual 111.50 105.36 6.14 1.50e+00 4.44e-01 1.68e+01 angle pdb=" N LYSCa 65 " pdb=" CA LYSCa 65 " pdb=" C LYSCa 65 " ideal model delta sigma weight residual 111.37 117.61 -6.24 1.64e+00 3.72e-01 1.45e+01 angle pdb=" N THRDa 97 " pdb=" CA THRDa 97 " pdb=" C THRDa 97 " ideal model delta sigma weight residual 111.37 116.24 -4.87 1.65e+00 3.67e-01 8.72e+00 angle pdb=" N GLYBa 105 " pdb=" CA GLYBa 105 " pdb=" C GLYBa 105 " ideal model delta sigma weight residual 113.18 119.23 -6.05 2.37e+00 1.78e-01 6.52e+00 ... (remaining 21970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.97: 6822 32.97 - 65.95: 1485 65.95 - 98.92: 47 98.92 - 131.90: 1 131.90 - 164.87: 2 Dihedral angle restraints: 8357 sinusoidal: 5036 harmonic: 3321 Sorted by residual: dihedral pdb=" C4' DC I 52 " pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " pdb=" P DC I 53 " ideal model delta sinusoidal sigma weight residual 220.00 55.13 164.87 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DT I -59 " pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sinusoidal sigma weight residual 220.00 58.25 161.75 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" CA ARGDa 96 " pdb=" C ARGDa 96 " pdb=" N THRDa 97 " pdb=" CA THRDa 97 " ideal model delta harmonic sigma weight residual 180.00 -161.67 -18.33 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 8354 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1547 0.033 - 0.065: 755 0.065 - 0.098: 175 0.098 - 0.130: 61 0.130 - 0.163: 13 Chirality restraints: 2551 Sorted by residual: chirality pdb=" CA PROBa 51 " pdb=" N PROBa 51 " pdb=" C PROBa 51 " pdb=" CB PROBa 51 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.62e-01 chirality pdb=" P DC I 53 " pdb=" OP1 DC I 53 " pdb=" OP2 DC I 53 " pdb=" O5' DC I 53 " both_signs ideal model delta sigma weight residual True 2.35 -2.50 -0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CB ILEBa 90 " pdb=" CA ILEBa 90 " pdb=" CG1 ILEBa 90 " pdb=" CG2 ILEBa 90 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.30e-01 ... (remaining 2548 not shown) Planarity restraints: 1789 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J -34 " 0.030 2.00e-02 2.50e+03 1.23e-02 4.52e+00 pdb=" N9 DG J -34 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DG J -34 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DG J -34 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG J -34 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG J -34 " 0.005 2.00e-02 2.50e+03 pdb=" O6 DG J -34 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DG J -34 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG J -34 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG J -34 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DG J -34 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DG J -34 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEUAb 109 " -0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PROAb 110 " 0.087 5.00e-02 4.00e+02 pdb=" CA PROAb 110 " -0.026 5.00e-02 4.00e+02 pdb=" CD PROAb 110 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SEREa 492 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PROEa 493 " 0.084 5.00e-02 4.00e+02 pdb=" CA PROEa 493 " -0.025 5.00e-02 4.00e+02 pdb=" CD PROEa 493 " -0.027 5.00e-02 4.00e+02 ... (remaining 1786 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 392 2.66 - 3.22: 12003 3.22 - 3.78: 22219 3.78 - 4.34: 28052 4.34 - 4.90: 42861 Nonbonded interactions: 105527 Sorted by model distance: nonbonded pdb=" O THREb 601 " pdb=" ND1 HISEb 602 " model vdw 2.106 3.120 nonbonded pdb=" OP1 DG J 48 " pdb=" OH TYRBb 41 " model vdw 2.276 3.040 nonbonded pdb=" O SEREb 612 " pdb=" OG SEREb 612 " model vdw 2.283 3.040 nonbonded pdb=" OG SERDb 48 " pdb=" N GLYDb 49 " model vdw 2.295 3.120 nonbonded pdb=" OD1 ASNEa 421 " pdb=" N HISEa 422 " model vdw 2.367 3.120 ... (remaining 105522 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 'Aa' and (resid 14 through 71 or (resid 72 through 73 and (name N or name \ CA or name C or name O or name CB )) or resid 74 through 95 or (resid 96 and (n \ ame N or name CA or name C or name O or name CB )) or resid 97 through 110 or (r \ esid 111 and (name N or name CA or name C or name O or name CB )) or resid 112 t \ hrough 118)) selection = (chain 'Ab' and ((resid 14 through 16 and (name N or name CA or name C or name O \ or name CB )) or resid 17 through 36 or (resid 37 and (name N or name CA or nam \ e C or name O or name CB )) or resid 38 through 92 or (resid 93 and (name N or n \ ame CA or name C or name O or name CB )) or resid 94 through 118)) } ncs_group { reference = (chain 'Ba' and (resid 34 through 105 or (resid 106 and (name N or name CA or na \ me C or name O or name CB )) or resid 107 through 125)) selection = (chain 'Bb' and (resid 34 through 42 or (resid 43 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ )) or resid 44 through 85 or (resid 86 and (name N or name CA or n \ ame C or name O or name CB )) or resid 87 through 123 or (resid 124 through 125 \ and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'Ca' and (resid 39 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 77 or (resid 78 and (name N or na \ me CA or name C or name O or name CB )) or resid 79 or (resid 80 and (name N or \ name CA or name C or name O or name CB )) or resid 81 through 106 or (resid 107 \ and (name N or name CA or name C or name O or name CB )) or resid 108 through 13 \ 4)) selection = (chain 'Cb' and (resid 39 through 115 or (resid 116 and (name N or name CA or na \ me C or name O or name CB )) or resid 117 through 134)) } ncs_group { reference = (chain 'Da' and (resid 25 through 74 or (resid 75 and (name N or name CA or name \ C or name O or name CB )) or resid 76 through 101)) selection = (chain 'Db' and resid 25 through 101) } 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 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: 3.090 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: 0.170 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 13.220 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 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 : 0.007 0.059 15284 Z= 0.318 Angle : 0.633 6.426 21975 Z= 0.388 Chirality : 0.041 0.163 2551 Planarity : 0.005 0.050 1789 Dihedral : 27.066 164.874 6211 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 6.72 % Allowed : 18.53 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.87 (0.22), residues: 1123 helix: -0.64 (0.19), residues: 614 sheet: -1.32 (0.77), residues: 51 loop : -3.85 (0.22), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGBb 34 TYR 0.017 0.002 TYRBa 38 PHE 0.013 0.002 PHEFa 4 TRP 0.017 0.002 TRPEb 752 HIS 0.005 0.001 HISAb 32 Details of bonding type rmsd covalent geometry : bond 0.00708 (15284) covalent geometry : angle 0.63315 (21975) hydrogen bonds : bond 0.15969 ( 509) hydrogen bonds : angle 4.94922 ( 1417) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 151 time to evaluate : 0.293 Fit side-chains REVERT: Ca 132 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8210 (mtp180) REVERT: Ba 58 LYS cc_start: 0.8244 (mmmt) cc_final: 0.7495 (ttmm) REVERT: Ba 100 ARG cc_start: 0.7631 (ttm170) cc_final: 0.7429 (mtm-85) REVERT: Aa 72 ARG cc_start: 0.7833 (tmm-80) cc_final: 0.7536 (ttp80) REVERT: Aa 74 ASN cc_start: 0.8687 (t0) cc_final: 0.8436 (t0) REVERT: Bb 100 ARG cc_start: 0.7757 (mtp180) cc_final: 0.7557 (mtm-85) REVERT: Cb 43 ARG cc_start: 0.8170 (ptp-110) cc_final: 0.7914 (mtm-85) REVERT: Cb 57 LYS cc_start: 0.8286 (ttmt) cc_final: 0.7921 (ttmm) REVERT: Cb 81 THR cc_start: 0.8912 (m) cc_final: 0.8682 (p) REVERT: Db 36 ARG cc_start: 0.7027 (OUTLIER) cc_final: 0.6620 (mtt180) outliers start: 54 outliers final: 25 residues processed: 193 average time/residue: 0.1328 time to fit residues: 35.6229 Evaluate side-chains 131 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ca residue 62 LEU Chi-restraints excluded: chain Ca residue 63 ILE Chi-restraints excluded: chain Ca residue 77 GLN Chi-restraints excluded: chain Ca residue 81 THR Chi-restraints excluded: chain Ca residue 132 ARG Chi-restraints excluded: chain Ba residue 43 TYR Chi-restraints excluded: chain Ba residue 53 THR Chi-restraints excluded: chain Ba residue 90 ILE Chi-restraints excluded: chain Aa residue 63 ILE Chi-restraints excluded: chain Bb residue 50 HIS Chi-restraints excluded: chain Bb residue 89 THR Chi-restraints excluded: chain Da residue 50 LEU Chi-restraints excluded: chain Da residue 51 ILE Chi-restraints excluded: chain Da residue 60 LYS Chi-restraints excluded: chain Ab residue 60 THR Chi-restraints excluded: chain Ab residue 94 LEU Chi-restraints excluded: chain Cb residue 119 THR Chi-restraints excluded: chain Db residue 30 ILE Chi-restraints excluded: chain Db residue 31 THR Chi-restraints excluded: chain Db residue 36 ARG Chi-restraints excluded: chain Ea residue 426 THR Chi-restraints excluded: chain Ea residue 485 SER Chi-restraints excluded: chain Fa residue 3 ILE Chi-restraints excluded: chain Fa residue 36 ILE Chi-restraints excluded: chain Eb residue 656 SER Chi-restraints excluded: chain Eb residue 735 TYR Chi-restraints excluded: chain Eb residue 746 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ba 50 HIS Bb 64 ASN Da 28 GLN Db 19 HIS ** Ea 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ea 455 HIS Ea 462 HIS Ea 500 ASN Eb 697 GLN Eb 719 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.168374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.120986 restraints weight = 18278.940| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.98 r_work: 0.2967 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15284 Z= 0.207 Angle : 0.577 5.850 21975 Z= 0.334 Chirality : 0.037 0.151 2551 Planarity : 0.005 0.085 1789 Dihedral : 29.242 165.441 4450 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.60 % Allowed : 21.89 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.25), residues: 1123 helix: 0.68 (0.21), residues: 632 sheet: -0.95 (0.75), residues: 53 loop : -3.34 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGEa 423 TYR 0.012 0.001 TYRAa 51 PHE 0.016 0.002 PHECa 79 TRP 0.016 0.001 TRPEb 752 HIS 0.006 0.001 HISCa 40 Details of bonding type rmsd covalent geometry : bond 0.00480 (15284) covalent geometry : angle 0.57685 (21975) hydrogen bonds : bond 0.07894 ( 509) hydrogen bonds : angle 3.37945 ( 1417) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 105 time to evaluate : 0.426 Fit side-chains REVERT: Ba 58 LYS cc_start: 0.8590 (mmmt) cc_final: 0.7867 (ttmm) REVERT: Ba 100 ARG cc_start: 0.8380 (ttm170) cc_final: 0.7911 (ttp-170) REVERT: Ba 114 GLU cc_start: 0.8085 (tp30) cc_final: 0.7668 (mm-30) REVERT: Aa 72 ARG cc_start: 0.8064 (tmm-80) cc_final: 0.7800 (ttp-110) REVERT: Ab 65 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8110 (tt0) REVERT: Cb 43 ARG cc_start: 0.8459 (ptp-110) cc_final: 0.8200 (mtm-85) REVERT: Cb 57 LYS cc_start: 0.8623 (ttmt) cc_final: 0.8357 (ttpp) REVERT: Cb 77 GLN cc_start: 0.8282 (tt0) cc_final: 0.8076 (tm-30) REVERT: Ea 451 ASN cc_start: 0.8916 (m-40) cc_final: 0.8576 (m110) REVERT: Ea 512 TYR cc_start: 0.7941 (OUTLIER) cc_final: 0.6857 (t80) outliers start: 37 outliers final: 23 residues processed: 136 average time/residue: 0.1546 time to fit residues: 29.3242 Evaluate side-chains 116 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ca residue 77 GLN Chi-restraints excluded: chain Ca residue 111 CYS Chi-restraints excluded: chain Ba residue 43 TYR Chi-restraints excluded: chain Ba residue 53 THR Chi-restraints excluded: chain Ba residue 90 ILE Chi-restraints excluded: chain Da residue 51 ILE Chi-restraints excluded: chain Da residue 60 LYS Chi-restraints excluded: chain Da residue 85 MET Chi-restraints excluded: chain Ab residue 80 ILE Chi-restraints excluded: chain Cb residue 75 ILE Chi-restraints excluded: chain Cb residue 111 CYS Chi-restraints excluded: chain Cb residue 119 THR Chi-restraints excluded: chain Db residue 31 THR Chi-restraints excluded: chain Db residue 51 ILE Chi-restraints excluded: chain Db residue 74 THR Chi-restraints excluded: chain Ea residue 452 VAL Chi-restraints excluded: chain Ea residue 483 VAL Chi-restraints excluded: chain Ea residue 505 ILE Chi-restraints excluded: chain Ea residue 512 TYR Chi-restraints excluded: chain Ea residue 527 VAL Chi-restraints excluded: chain Fa residue 36 ILE Chi-restraints excluded: chain Eb residue 709 VAL Chi-restraints excluded: chain Eb residue 735 TYR Chi-restraints excluded: chain Eb residue 746 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 94 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 102 optimal weight: 0.0570 chunk 106 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 104 optimal weight: 20.0000 chunk 81 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Fa 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.165708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.112785 restraints weight = 18400.225| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.76 r_work: 0.2916 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15284 Z= 0.229 Angle : 0.576 6.069 21975 Z= 0.331 Chirality : 0.037 0.181 2551 Planarity : 0.005 0.087 1789 Dihedral : 29.417 170.336 4420 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.48 % Allowed : 23.38 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.25), residues: 1123 helix: 0.97 (0.21), residues: 636 sheet: -0.81 (0.74), residues: 53 loop : -3.08 (0.26), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGEa 423 TYR 0.013 0.001 TYRAa 51 PHE 0.018 0.002 PHECa 79 TRP 0.012 0.001 TRPEb 752 HIS 0.004 0.001 HISCa 40 Details of bonding type rmsd covalent geometry : bond 0.00538 (15284) covalent geometry : angle 0.57583 (21975) hydrogen bonds : bond 0.08477 ( 509) hydrogen bonds : angle 3.34175 ( 1417) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.421 Fit side-chains REVERT: Ba 58 LYS cc_start: 0.8513 (mmmt) cc_final: 0.7784 (ttmm) REVERT: Ba 60 MET cc_start: 0.8418 (mmm) cc_final: 0.8166 (mmt) REVERT: Ba 100 ARG cc_start: 0.8377 (ttm170) cc_final: 0.7779 (ttp-170) REVERT: Ba 114 GLU cc_start: 0.8070 (tp30) cc_final: 0.7586 (mm-30) REVERT: Aa 72 ARG cc_start: 0.8045 (tmm-80) cc_final: 0.7628 (ttp80) REVERT: Ab 65 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8133 (tt0) REVERT: Ab 93 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7748 (mt-10) REVERT: Cb 43 ARG cc_start: 0.8415 (ptp-110) cc_final: 0.8010 (mtp85) REVERT: Cb 57 LYS cc_start: 0.8608 (ttmt) cc_final: 0.8272 (ttmm) REVERT: Cb 77 GLN cc_start: 0.8261 (tt0) cc_final: 0.7901 (tm-30) REVERT: Ea 528 ASP cc_start: 0.9040 (t0) cc_final: 0.8833 (t0) outliers start: 36 outliers final: 29 residues processed: 130 average time/residue: 0.1208 time to fit residues: 22.4477 Evaluate side-chains 124 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ca residue 77 GLN Chi-restraints excluded: chain Ca residue 81 THR Chi-restraints excluded: chain Ca residue 111 CYS Chi-restraints excluded: chain Ca residue 113 ILE Chi-restraints excluded: chain Ca residue 124 ASP Chi-restraints excluded: chain Ba residue 43 TYR Chi-restraints excluded: chain Ba residue 53 THR Chi-restraints excluded: chain Aa residue 20 SER Chi-restraints excluded: chain Da residue 60 LYS Chi-restraints excluded: chain Da residue 85 MET Chi-restraints excluded: chain Ab residue 80 ILE Chi-restraints excluded: chain Ab residue 103 ILE Chi-restraints excluded: chain Cb residue 75 ILE Chi-restraints excluded: chain Cb residue 111 CYS Chi-restraints excluded: chain Cb residue 119 THR Chi-restraints excluded: chain Db residue 31 THR Chi-restraints excluded: chain Db residue 51 ILE Chi-restraints excluded: chain Db residue 74 THR Chi-restraints excluded: chain Db residue 85 MET Chi-restraints excluded: chain Ea residue 452 VAL Chi-restraints excluded: chain Ea residue 483 VAL Chi-restraints excluded: chain Ea residue 505 ILE Chi-restraints excluded: chain Ea residue 527 VAL Chi-restraints excluded: chain Fa residue 30 ILE Chi-restraints excluded: chain Fa residue 36 ILE Chi-restraints excluded: chain Eb residue 709 VAL Chi-restraints excluded: chain Eb residue 735 TYR Chi-restraints excluded: chain Eb residue 746 VAL Chi-restraints excluded: chain Eb residue 757 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.189 > 50: distance: 77 - 80: 12.976 distance: 80 - 81: 3.974 distance: 81 - 82: 11.451 distance: 81 - 84: 12.844 distance: 82 - 83: 3.968 distance: 82 - 87: 8.466 distance: 84 - 85: 12.743 distance: 84 - 86: 21.358 distance: 87 - 88: 8.077 distance: 88 - 89: 6.645 distance: 88 - 91: 11.717 distance: 89 - 90: 14.664 distance: 89 - 94: 6.815 distance: 91 - 92: 10.504 distance: 91 - 93: 8.719 distance: 94 - 95: 13.910 distance: 95 - 96: 14.713 distance: 95 - 98: 16.039 distance: 96 - 97: 34.352 distance: 96 - 102: 29.133 distance: 98 - 99: 27.554 distance: 98 - 100: 14.377 distance: 99 - 101: 14.888 distance: 102 - 103: 14.130 distance: 103 - 104: 29.259 distance: 103 - 106: 17.924 distance: 104 - 105: 6.905 distance: 104 - 107: 32.406 distance: 107 - 108: 13.475 distance: 108 - 109: 26.033 distance: 108 - 111: 13.757 distance: 109 - 110: 9.446 distance: 109 - 116: 19.615 distance: 111 - 112: 12.515 distance: 112 - 113: 14.268 distance: 113 - 114: 12.986 distance: 113 - 115: 16.099 distance: 116 - 117: 17.081 distance: 118 - 119: 11.321 distance: 118 - 120: 8.919 distance: 120 - 121: 3.792 distance: 121 - 122: 3.288 distance: 122 - 123: 4.655 distance: 124 - 125: 5.003 distance: 125 - 126: 6.776 distance: 125 - 128: 6.137 distance: 126 - 127: 3.665 distance: 126 - 131: 11.522 distance: 128 - 129: 7.378 distance: 128 - 130: 16.538 distance: 131 - 132: 4.282 distance: 132 - 133: 5.592 distance: 132 - 135: 6.983 distance: 133 - 134: 6.391 distance: 133 - 139: 12.545 distance: 135 - 136: 7.454 distance: 136 - 137: 6.529 distance: 136 - 138: 8.336 distance: 139 - 140: 14.342 distance: 139 - 145: 5.514 distance: 140 - 141: 14.279 distance: 140 - 143: 5.062 distance: 141 - 142: 8.671 distance: 141 - 146: 7.668 distance: 143 - 144: 5.529 distance: 144 - 145: 9.959