Starting phenix.real_space_refine on Thu Aug 6 07:16:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8off_16859/08_2026/8off_16859.cif Found real_map, /net/cci-nas-00/data/ceres_data/8off_16859/08_2026/8off_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_2026/8off_16859.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8off_16859/08_2026/8off_16859.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8off_16859/08_2026/8off_16859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8off_16859/08_2026/8off_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-2.2rc3-6140/lib/python3.11/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: 2.88, per 1000 atoms: 0.20 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: 1.03 Conformation dependent library (CDL) restraints added in 369.9 milliseconds 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: 1.63 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: 2.36 Time building geometry restraints manager: 1.44 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 1.20e-02 6.94e+03 2.43e+01 bond pdb=" C3' DG J -49 " pdb=" C2' DG J -49 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.49e+01 bond pdb=" C3' DG J 27 " pdb=" O3' DG J 27 " ideal model delta sigma weight residual 1.435 1.389 0.046 1.30e-02 5.92e+03 1.24e+01 bond pdb=" C3' DG I 48 " pdb=" O3' DG I 48 " ideal model delta sigma weight residual 1.435 1.389 0.046 1.30e-02 5.92e+03 1.23e+01 bond pdb=" C3' DA I 65 " pdb=" C2' DA I 65 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 ... (remaining 15279 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 19723 1.29 - 2.57: 2062 2.57 - 3.86: 160 3.86 - 5.14: 24 5.14 - 6.43: 6 Bond angle restraints: 21975 Sorted by residual: angle pdb=" O4' DT J -59 " pdb=" C4' DT J -59 " pdb=" C3' DT J -59 " ideal model delta sigma weight residual 106.00 102.79 3.21 6.00e-01 2.78e+00 2.87e+01 angle pdb=" O4' DG I 64 " pdb=" C4' DG I 64 " pdb=" C3' DG I 64 " ideal model delta sigma weight residual 106.00 102.84 3.16 6.00e-01 2.78e+00 2.77e+01 angle pdb=" O4' DA J -33 " pdb=" C4' DA J -33 " pdb=" C3' DA J -33 " ideal model delta sigma weight residual 106.00 103.15 2.85 6.00e-01 2.78e+00 2.26e+01 angle pdb=" N3 DT J -42 " pdb=" C4 DT J -42 " pdb=" O4 DT J -42 " ideal model delta sigma weight residual 119.90 122.69 -2.79 6.00e-01 2.78e+00 2.17e+01 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 ... (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 - 0.038: 1502 0.038 - 0.076: 735 0.076 - 0.115: 259 0.115 - 0.153: 50 0.153 - 0.191: 5 Chirality restraints: 2551 Sorted by residual: chirality pdb=" C3' DC J 0 " pdb=" C4' DC J 0 " pdb=" O3' DC J 0 " pdb=" C2' DC J 0 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.13e-01 chirality pdb=" C3' DC I 52 " pdb=" C4' DC I 52 " pdb=" O3' DC I 52 " pdb=" C2' DC I 52 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.87e-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 2.34 -2.50 -0.17 2.00e-01 2.50e+01 7.17e-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: 1.920 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: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.030 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 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 : 0.008 0.059 15284 Z= 0.647 Angle : 0.774 6.426 21975 Z= 0.663 Chirality : 0.049 0.191 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 are 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/Z covalent geometry : bond 0.00796 / 0.65 (15284) covalent geometry : angle 0.77354 / 0.66 (21975) hydrogen bonds : bond 0.15969 / 17.64 ( 509) hydrogen bonds : angle 4.94922 / 6.39 ( 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 : 0.267 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: 0.6684 (mtt180) outliers start: 54 outliers final: 25 residues processed: 193 average time/residue: 0.1319 time to fit residues: 35.5825 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 : 0.343 ------------------------------------------------------------------------------- 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: 20.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 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... 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 Eb 697 GLN Eb 719 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.169117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.122078 restraints weight = 18165.662| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.97 r_work: 0.2985 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 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 = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15284 Z= 0.206 Angle : 0.651 6.888 21975 Z= 0.381 Chirality : 0.047 0.358 2551 Planarity : 0.006 0.089 1789 Dihedral : 29.451 168.541 4450 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.73 % Allowed : 22.39 % Favored : 72.89 % 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 are not related in a simple way. whole: -1.28 (0.25), residues: 1123 helix: 0.68 (0.21), residues: 632 sheet: 0.12 (0.81), residues: 47 loop : -3.39 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARGAa 30 TYR 0.013 0.002 TYRDa 52 PHE 0.012 0.002 PHEEb 759 TRP 0.013 0.001 TRPEb 752 HIS 0.007 0.001 HISCa 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.21 (15284) covalent geometry : angle 0.65083 / 0.38 (21975) hydrogen bonds : bond 0.08343 / 9.50 ( 509) hydrogen bonds : angle 3.48824 / 4.49 ( 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 149 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 111 time to evaluate : 0.414 Fit side-chains REVERT: Ca 62 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7906 (pp) REVERT: Ba 58 LYS cc_start: 0.8567 (mmmt) cc_final: 0.7829 (ttmm) REVERT: Ba 100 ARG cc_start: 0.8391 (ttm170) cc_final: 0.8001 (mtm-85) REVERT: Aa 72 ARG cc_start: 0.8171 (tmm-80) cc_final: 0.7949 (ttp-110) REVERT: Aa 74 ASN cc_start: 0.8757 (t0) cc_final: 0.8440 (t0) REVERT: Ab 62 GLU cc_start: 0.8046 (tp30) cc_final: 0.7825 (tp30) REVERT: Ab 65 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8174 (tt0) REVERT: Cb 43 ARG cc_start: 0.8511 (ptp-110) cc_final: 0.8225 (mtm-85) REVERT: Cb 57 LYS cc_start: 0.8565 (ttmt) cc_final: 0.8317 (ttpp) REVERT: Ea 451 ASN cc_start: 0.8922 (m-40) cc_final: 0.8650 (m110) outliers start: 38 outliers final: 26 residues processed: 141 average time/residue: 0.1375 time to fit residues: 27.2850 Evaluate side-chains 126 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ca residue 62 LEU 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 Ba residue 43 TYR Chi-restraints excluded: chain Ba residue 53 THR Chi-restraints excluded: chain Ba residue 55 ILE Chi-restraints excluded: chain Aa residue 20 SER Chi-restraints excluded: chain Bb residue 89 THR 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 74 THR Chi-restraints excluded: chain Ea residue 452 VAL Chi-restraints excluded: chain Ea residue 475 LEU Chi-restraints excluded: chain Ea residue 477 LEU 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 36 ILE 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: 3.9990 chunk 32 optimal weight: 0.0040 chunk 102 optimal weight: 7.9990 chunk 106 optimal weight: 30.0000 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 104 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 128 optimal weight: 20.0000 chunk 122 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 overall best weight: 1.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Ea 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ea 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Fa 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.170173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.123587 restraints weight = 18323.420| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.03 r_work: 0.3005 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15284 Z= 0.164 Angle : 0.564 5.638 21975 Z= 0.334 Chirality : 0.042 0.335 2551 Planarity : 0.005 0.084 1789 Dihedral : 29.412 166.656 4420 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.48 % Allowed : 23.01 % Favored : 72.51 % 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 are not related in a simple way. whole: -0.61 (0.25), residues: 1123 helix: 1.23 (0.21), residues: 630 sheet: -0.37 (0.78), residues: 53 loop : -3.02 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGEa 423 TYR 0.010 0.001 TYRAa 51 PHE 0.015 0.001 PHEEb 759 TRP 0.010 0.001 TRPEb 752 HIS 0.005 0.001 HISEa 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.16 (15284) covalent geometry : angle 0.56355 / 0.33 (21975) hydrogen bonds : bond 0.07097 / 8.11 ( 509) hydrogen bonds : angle 3.19716 / 4.07 ( 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 138 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 102 time to evaluate : 0.395 Fit side-chains REVERT: Ba 58 LYS cc_start: 0.8549 (mmmt) cc_final: 0.7834 (ttmm) REVERT: Ba 80 ARG cc_start: 0.8282 (ttm110) cc_final: 0.7931 (mtm180) REVERT: Ba 100 ARG cc_start: 0.8392 (ttm170) cc_final: 0.7933 (mtm-85) REVERT: Ba 114 GLU cc_start: 0.8005 (tp30) cc_final: 0.7696 (mm-30) REVERT: Aa 72 ARG cc_start: 0.8031 (tmm-80) cc_final: 0.7751 (ttp-110) REVERT: Aa 74 ASN cc_start: 0.8737 (t0) cc_final: 0.8397 (t0) REVERT: Ab 62 GLU cc_start: 0.7993 (tp30) cc_final: 0.7737 (tp30) REVERT: Ab 65 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8117 (tt0) REVERT: Cb 43 ARG cc_start: 0.8426 (ptp-110) cc_final: 0.8153 (mtm-85) REVERT: Cb 57 LYS cc_start: 0.8579 (ttmt) cc_final: 0.8320 (ttpp) REVERT: Cb 110 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8601 (tp) REVERT: Ea 512 TYR cc_start: 0.7862 (OUTLIER) cc_final: 0.6948 (t80) outliers start: 36 outliers final: 23 residues processed: 132 average time/residue: 0.1332 time to fit residues: 25.1069 Evaluate side-chains 123 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 119 THR Chi-restraints excluded: chain Ba residue 43 TYR Chi-restraints excluded: chain Ba residue 53 THR Chi-restraints excluded: chain Ba residue 55 ILE 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 Cb residue 75 ILE Chi-restraints excluded: chain Cb residue 110 LEU Chi-restraints excluded: chain Cb residue 111 CYS Chi-restraints excluded: chain Cb residue 119 THR 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 512 TYR Chi-restraints excluded: chain Ea residue 527 VAL Chi-restraints excluded: chain Fa residue 36 ILE 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 ************** Weight determination summary: number of chunks: 137 random chunks: chunk 42 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 23 optimal weight: 0.3980 chunk 75 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 117 optimal weight: 0.0270 chunk 26 optimal weight: 0.5980 chunk 28 optimal weight: 0.3980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ea 500 ASN Ea 502 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.172659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.120423 restraints weight = 18377.203| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.66 r_work: 0.3087 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15284 Z= 0.132 Angle : 0.515 6.289 21975 Z= 0.307 Chirality : 0.040 0.348 2551 Planarity : 0.005 0.090 1789 Dihedral : 29.316 169.995 4416 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.48 % Allowed : 24.25 % Favored : 71.27 % 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 are not related in a simple way. whole: 0.01 (0.26), residues: 1123 helix: 1.66 (0.21), residues: 635 sheet: 0.44 (0.83), residues: 47 loop : -2.71 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGEa 423 TYR 0.009 0.001 TYRDb 52 PHE 0.014 0.001 PHEEb 759 TRP 0.009 0.001 TRPEb 752 HIS 0.004 0.001 HISCa 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.13 (15284) covalent geometry : angle 0.51491 / 0.31 (21975) hydrogen bonds : bond 0.05019 / 5.82 ( 509) hydrogen bonds : angle 2.84900 / 3.64 ( 1417) *********************** REFINEMENT MACRO_CYCLE 4 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 141 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 0.310 Fit side-chains REVERT: Ba 58 LYS cc_start: 0.8437 (mmmt) cc_final: 0.7719 (ttmm) REVERT: Ba 80 ARG cc_start: 0.8116 (ttm110) cc_final: 0.7720 (mtm180) REVERT: Ba 100 ARG cc_start: 0.8300 (ttm170) cc_final: 0.7817 (mtm-85) REVERT: Ba 114 GLU cc_start: 0.7860 (tp30) cc_final: 0.7572 (mm-30) REVERT: Ab 62 GLU cc_start: 0.7786 (tp30) cc_final: 0.7498 (tp30) REVERT: Ab 65 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7955 (tt0) REVERT: Cb 57 LYS cc_start: 0.8473 (ttmt) cc_final: 0.8131 (ttmm) REVERT: Cb 77 GLN cc_start: 0.7964 (tt0) cc_final: 0.7747 (tm-30) REVERT: Ea 512 TYR cc_start: 0.7717 (OUTLIER) cc_final: 0.6686 (t80) outliers start: 36 outliers final: 23 residues processed: 131 average time/residue: 0.1398 time to fit residues: 26.0033 Evaluate side-chains 123 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ca residue 77 GLN Chi-restraints excluded: chain Ca residue 113 ILE 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 20 SER Chi-restraints excluded: chain Bb residue 36 GLU Chi-restraints excluded: chain Da residue 60 LYS Chi-restraints excluded: chain Da residue 85 MET Chi-restraints excluded: chain Ab residue 94 LEU 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 74 THR Chi-restraints excluded: chain Ea residue 452 VAL Chi-restraints excluded: chain Ea residue 475 LEU Chi-restraints excluded: chain Ea residue 483 VAL Chi-restraints excluded: chain Ea residue 512 TYR Chi-restraints excluded: chain Fa residue 30 ILE Chi-restraints excluded: chain Fa residue 36 ILE Chi-restraints excluded: chain Eb residue 659 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 92 optimal weight: 8.9990 chunk 41 optimal weight: 0.5980 chunk 6 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 117 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 125 optimal weight: 20.0000 chunk 110 optimal weight: 0.3980 chunk 114 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Eb 731 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.166862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.115067 restraints weight = 18221.286| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.87 r_work: 0.2935 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2258 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= 0.210 Angle : 0.590 5.623 21975 Z= 0.339 Chirality : 0.044 0.342 2551 Planarity : 0.005 0.087 1789 Dihedral : 29.552 172.738 4415 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 4.23 % Allowed : 24.63 % Favored : 71.14 % 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 are not related in a simple way. whole: -0.24 (0.26), residues: 1123 helix: 1.38 (0.21), residues: 638 sheet: 0.09 (0.80), residues: 48 loop : -2.69 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGEa 423 TYR 0.012 0.002 TYRAa 51 PHE 0.020 0.002 PHECa 79 TRP 0.008 0.001 TRPEb 752 HIS 0.004 0.001 HISEa 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.21 (15284) covalent geometry : angle 0.59002 / 0.34 (21975) hydrogen bonds : bond 0.08187 / 9.27 ( 509) hydrogen bonds : angle 3.17033 / 4.09 ( 1417) *********************** REFINEMENT MACRO_CYCLE 5 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 135 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.283 Fit side-chains REVERT: Ba 58 LYS cc_start: 0.8505 (mmmt) cc_final: 0.7749 (ttmm) REVERT: Ba 100 ARG cc_start: 0.8349 (ttm170) cc_final: 0.7728 (ttp-170) REVERT: Ba 114 GLU cc_start: 0.8025 (tp30) cc_final: 0.7557 (mm-30) REVERT: Aa 72 ARG cc_start: 0.7905 (ttp-110) cc_final: 0.7554 (ttp80) REVERT: Ab 65 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8115 (tt0) REVERT: Cb 57 LYS cc_start: 0.8649 (ttmt) cc_final: 0.8396 (ttpp) REVERT: Cb 77 GLN cc_start: 0.8101 (tt0) cc_final: 0.7715 (tm-30) REVERT: Db 92 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8257 (ttpt) REVERT: Ea 512 TYR cc_start: 0.7804 (OUTLIER) cc_final: 0.6713 (t80) REVERT: Eb 761 ASP cc_start: 0.8895 (t0) cc_final: 0.8674 (t0) outliers start: 34 outliers final: 26 residues processed: 126 average time/residue: 0.1139 time to fit residues: 20.6761 Evaluate side-chains 125 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 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 20 SER Chi-restraints excluded: chain Bb residue 36 GLU Chi-restraints excluded: chain Da residue 60 LYS Chi-restraints excluded: chain Da residue 85 MET Chi-restraints excluded: chain Ab residue 94 LEU Chi-restraints excluded: chain Ab residue 103 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 92 LYS Chi-restraints excluded: chain Ea residue 452 VAL Chi-restraints excluded: chain Ea residue 483 VAL 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 Chi-restraints excluded: chain Eb residue 757 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 119 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 chunk 51 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ea 500 ASN Fa 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.168784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.116529 restraints weight = 18279.233| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.77 r_work: 0.2997 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 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 : 0.003 0.028 15284 Z= 0.154 Angle : 0.531 5.618 21975 Z= 0.312 Chirality : 0.041 0.344 2551 Planarity : 0.005 0.087 1789 Dihedral : 29.496 175.232 4415 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.85 % Allowed : 23.88 % Favored : 71.27 % 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 are not related in a simple way. whole: -0.05 (0.26), residues: 1123 helix: 1.53 (0.21), residues: 639 sheet: 0.11 (0.83), residues: 42 loop : -2.56 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGEa 423 TYR 0.010 0.001 TYRDa 52 PHE 0.011 0.001 PHECa 79 TRP 0.008 0.001 TRPEb 752 HIS 0.004 0.001 HISEa 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.15 (15284) covalent geometry : angle 0.53135 / 0.31 (21975) hydrogen bonds : bond 0.06810 / 7.80 ( 509) hydrogen bonds : angle 3.00055 / 3.84 ( 1417) *********************** REFINEMENT MACRO_CYCLE 6 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 139 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 100 time to evaluate : 0.358 Fit side-chains REVERT: Ba 58 LYS cc_start: 0.8452 (mmmt) cc_final: 0.7696 (ttmm) REVERT: Ba 100 ARG cc_start: 0.8254 (ttm170) cc_final: 0.7661 (mtm-85) REVERT: Ba 114 GLU cc_start: 0.7932 (tp30) cc_final: 0.7478 (mm-30) REVERT: Aa 72 ARG cc_start: 0.7784 (ttp-110) cc_final: 0.7530 (ttp80) REVERT: Ab 65 GLU cc_start: 0.8321 (tm-30) cc_final: 0.8058 (tt0) REVERT: Cb 57 LYS cc_start: 0.8598 (ttmt) cc_final: 0.8326 (ttpp) REVERT: Cb 77 GLN cc_start: 0.8002 (tt0) cc_final: 0.7646 (tm-30) REVERT: Ea 512 TYR cc_start: 0.7775 (OUTLIER) cc_final: 0.6648 (t80) outliers start: 39 outliers final: 32 residues processed: 128 average time/residue: 0.1079 time to fit residues: 20.4598 Evaluate side-chains 131 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 98 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ca residue 77 GLN Chi-restraints excluded: chain Ca residue 111 CYS Chi-restraints excluded: chain Ca residue 113 ILE Chi-restraints excluded: chain Ca residue 119 THR 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 20 SER Chi-restraints excluded: chain Aa residue 86 LEU Chi-restraints excluded: chain Bb residue 36 GLU Chi-restraints excluded: chain Da residue 60 LYS Chi-restraints excluded: chain Da residue 85 MET Chi-restraints excluded: chain Ab residue 94 LEU Chi-restraints excluded: chain Cb residue 75 ILE Chi-restraints excluded: chain Cb residue 91 MET 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 477 LEU Chi-restraints excluded: chain Ea residue 482 LEU Chi-restraints excluded: chain Ea residue 483 VAL Chi-restraints excluded: chain Ea residue 500 ASN 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 659 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 54 optimal weight: 0.6980 chunk 133 optimal weight: 20.0000 chunk 42 optimal weight: 0.9980 chunk 131 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ea 500 ASN Fa 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.169398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.115748 restraints weight = 18191.072| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.71 r_work: 0.3017 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15284 Z= 0.143 Angle : 0.519 5.257 21975 Z= 0.305 Chirality : 0.040 0.343 2551 Planarity : 0.004 0.089 1789 Dihedral : 29.469 177.195 4415 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.85 % Allowed : 24.25 % Favored : 70.90 % 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 are not related in a simple way. whole: 0.09 (0.26), residues: 1123 helix: 1.62 (0.21), residues: 639 sheet: 0.23 (0.84), residues: 42 loop : -2.46 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGEa 423 TYR 0.009 0.001 TYRDa 52 PHE 0.008 0.001 PHECa 79 TRP 0.007 0.001 TRPEb 752 HIS 0.004 0.001 HISEa 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.14 (15284) covalent geometry : angle 0.51933 / 0.31 (21975) hydrogen bonds : bond 0.06321 / 7.24 ( 509) hydrogen bonds : angle 2.94136 / 3.76 ( 1417) *********************** REFINEMENT MACRO_CYCLE 7 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 138 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 99 time to evaluate : 0.412 Fit side-chains REVERT: Ba 58 LYS cc_start: 0.8421 (mmmt) cc_final: 0.7662 (ttmm) REVERT: Ba 100 ARG cc_start: 0.8236 (ttm170) cc_final: 0.7650 (mtm-85) REVERT: Ba 114 GLU cc_start: 0.7916 (tp30) cc_final: 0.7456 (mm-30) REVERT: Aa 72 ARG cc_start: 0.7751 (ttp-110) cc_final: 0.7505 (ttp80) REVERT: Ab 65 GLU cc_start: 0.8279 (tm-30) cc_final: 0.8003 (tt0) REVERT: Cb 57 LYS cc_start: 0.8561 (ttmt) cc_final: 0.8301 (ttpp) REVERT: Cb 77 GLN cc_start: 0.7980 (tt0) cc_final: 0.7631 (tm-30) REVERT: Ea 512 TYR cc_start: 0.7799 (OUTLIER) cc_final: 0.6567 (t80) outliers start: 39 outliers final: 33 residues processed: 127 average time/residue: 0.1109 time to fit residues: 20.8979 Evaluate side-chains 129 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 95 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ca residue 77 GLN Chi-restraints excluded: chain Ca residue 113 ILE Chi-restraints excluded: chain Ca residue 119 THR 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 Ba residue 55 ILE Chi-restraints excluded: chain Ba residue 90 ILE Chi-restraints excluded: chain Aa residue 20 SER Chi-restraints excluded: chain Aa residue 86 LEU Chi-restraints excluded: chain Bb residue 36 GLU Chi-restraints excluded: chain Da residue 31 THR 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 94 LEU Chi-restraints excluded: chain Cb residue 75 ILE Chi-restraints excluded: chain Cb residue 91 MET 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 477 LEU Chi-restraints excluded: chain Ea residue 483 VAL 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 659 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 106 optimal weight: 20.0000 chunk 93 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 125 optimal weight: 20.0000 chunk 67 optimal weight: 0.0010 chunk 75 optimal weight: 1.9990 chunk 10 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 3 optimal weight: 30.0000 chunk 37 optimal weight: 1.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Ea 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Fa 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.168861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.117559 restraints weight = 18263.244| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.91 r_work: 0.2983 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 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 = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15284 Z= 0.154 Angle : 0.525 5.340 21975 Z= 0.307 Chirality : 0.040 0.343 2551 Planarity : 0.005 0.087 1789 Dihedral : 29.496 179.597 4415 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.60 % Allowed : 24.13 % Favored : 71.27 % 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 are not related in a simple way. whole: 0.13 (0.26), residues: 1123 helix: 1.65 (0.21), residues: 640 sheet: 0.22 (0.84), residues: 42 loop : -2.44 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGEa 423 TYR 0.009 0.001 TYRDa 52 PHE 0.011 0.001 PHECa 79 TRP 0.007 0.001 TRPEb 752 HIS 0.003 0.001 HISEa 462 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 (15284) covalent geometry : angle 0.52515 / 0.31 (21975) hydrogen bonds : bond 0.06635 / 7.59 ( 509) hydrogen bonds : angle 2.95500 / 3.78 ( 1417) *********************** REFINEMENT MACRO_CYCLE 8 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 131 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 94 time to evaluate : 0.370 Fit side-chains REVERT: Ba 58 LYS cc_start: 0.8429 (mmmt) cc_final: 0.7671 (ttmm) REVERT: Ba 100 ARG cc_start: 0.8272 (ttm170) cc_final: 0.7620 (ttp-170) REVERT: Ba 114 GLU cc_start: 0.7984 (tp30) cc_final: 0.7465 (mm-30) REVERT: Aa 72 ARG cc_start: 0.7766 (ttp-110) cc_final: 0.7479 (ttp80) REVERT: Ab 65 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7978 (tt0) REVERT: Cb 57 LYS cc_start: 0.8581 (ttmt) cc_final: 0.8329 (ttpp) REVERT: Cb 77 GLN cc_start: 0.7970 (tt0) cc_final: 0.7595 (tm-30) outliers start: 37 outliers final: 31 residues processed: 123 average time/residue: 0.1053 time to fit residues: 19.3366 Evaluate side-chains 123 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ca residue 77 GLN Chi-restraints excluded: chain Ca residue 119 THR 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 Ba residue 55 ILE Chi-restraints excluded: chain Ba residue 90 ILE Chi-restraints excluded: chain Aa residue 20 SER Chi-restraints excluded: chain Aa residue 86 LEU Chi-restraints excluded: chain Bb residue 36 GLU Chi-restraints excluded: chain Da residue 31 THR Chi-restraints excluded: chain Da residue 60 LYS Chi-restraints excluded: chain Da residue 85 MET Chi-restraints excluded: chain Ab residue 94 LEU 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 477 LEU Chi-restraints excluded: chain Ea residue 482 LEU Chi-restraints excluded: chain Ea residue 483 VAL Chi-restraints excluded: chain Ea residue 527 VAL Chi-restraints excluded: chain Fa residue 36 ILE Chi-restraints excluded: chain Eb residue 659 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 81 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 18 optimal weight: 0.0980 chunk 61 optimal weight: 0.4980 chunk 134 optimal weight: 20.0000 chunk 80 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 125 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 25 GLN Bb 50 HIS Fa 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.171997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.120107 restraints weight = 18358.170| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.72 r_work: 0.3070 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15284 Z= 0.123 Angle : 0.494 5.365 21975 Z= 0.293 Chirality : 0.038 0.339 2551 Planarity : 0.004 0.087 1789 Dihedral : 29.395 178.218 4415 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.11 % Allowed : 25.62 % Favored : 71.27 % 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 are not related in a simple way. whole: 0.52 (0.26), residues: 1123 helix: 1.96 (0.21), residues: 636 sheet: 0.55 (0.85), residues: 42 loop : -2.23 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGEa 423 TYR 0.008 0.001 TYRDa 52 PHE 0.006 0.001 PHEEb 759 TRP 0.008 0.001 TRPEb 752 HIS 0.002 0.001 HISCa 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.12 (15284) covalent geometry : angle 0.49407 / 0.29 (21975) hydrogen bonds : bond 0.05103 / 5.89 ( 509) hydrogen bonds : angle 2.76559 / 3.51 ( 1417) *********************** REFINEMENT MACRO_CYCLE 9 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 116 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.378 Fit side-chains REVERT: Ba 58 LYS cc_start: 0.8372 (mmmt) cc_final: 0.7627 (ttmm) REVERT: Ba 100 ARG cc_start: 0.8247 (ttm170) cc_final: 0.7644 (mtm-85) REVERT: Ba 114 GLU cc_start: 0.7938 (tp30) cc_final: 0.7507 (mm-30) REVERT: Ab 65 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7926 (tt0) REVERT: Cb 57 LYS cc_start: 0.8524 (ttmt) cc_final: 0.8263 (ttpp) REVERT: Cb 77 GLN cc_start: 0.7812 (tt0) cc_final: 0.7541 (tm-30) REVERT: Ea 512 TYR cc_start: 0.7726 (OUTLIER) cc_final: 0.6404 (t80) outliers start: 25 outliers final: 21 residues processed: 107 average time/residue: 0.1186 time to fit residues: 18.8213 Evaluate side-chains 112 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ca residue 77 GLN Chi-restraints excluded: chain Ca residue 113 ILE Chi-restraints excluded: chain Ca residue 119 THR 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 20 SER Chi-restraints excluded: chain Bb residue 36 GLU Chi-restraints excluded: chain Bb residue 50 HIS Chi-restraints excluded: chain Da residue 60 LYS Chi-restraints excluded: chain Da residue 85 MET Chi-restraints excluded: chain Cb residue 111 CYS Chi-restraints excluded: chain Cb residue 119 THR Chi-restraints excluded: chain Ea residue 452 VAL Chi-restraints excluded: chain Ea residue 477 LEU Chi-restraints excluded: chain Ea residue 483 VAL Chi-restraints excluded: chain Ea residue 512 TYR Chi-restraints excluded: chain Fa residue 36 ILE Chi-restraints excluded: chain Eb residue 662 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 132 optimal weight: 20.0000 chunk 120 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 78 optimal weight: 0.1980 chunk 107 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 35 optimal weight: 0.2980 chunk 96 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 0.1980 chunk 18 optimal weight: 0.4980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Fa 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.172587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.120332 restraints weight = 18241.161| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.69 r_work: 0.3073 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15284 Z= 0.119 Angle : 0.485 5.277 21975 Z= 0.288 Chirality : 0.038 0.337 2551 Planarity : 0.004 0.086 1789 Dihedral : 29.383 177.301 4415 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.86 % Allowed : 26.12 % Favored : 71.02 % 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 are not related in a simple way. whole: 0.69 (0.26), residues: 1123 helix: 2.10 (0.21), residues: 637 sheet: 0.67 (0.86), residues: 42 loop : -2.20 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGEa 423 TYR 0.006 0.001 TYRDa 52 PHE 0.007 0.001 PHEEb 759 TRP 0.008 0.001 TRPEb 752 HIS 0.009 0.001 HISBb 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00182 / 0.12 (15284) covalent geometry : angle 0.48469 / 0.29 (21975) hydrogen bonds : bond 0.04838 / 5.57 ( 509) hydrogen bonds : angle 2.71009 / 3.44 ( 1417) ********************** REFINEMENT MACRO_CYCLE 10 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 114 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.338 Fit side-chains REVERT: Ba 58 LYS cc_start: 0.8375 (mmmt) cc_final: 0.7642 (ttmm) REVERT: Ba 100 ARG cc_start: 0.8282 (ttm170) cc_final: 0.7703 (mtm-85) REVERT: Ba 114 GLU cc_start: 0.7948 (tp30) cc_final: 0.7560 (mm-30) REVERT: Ab 65 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7967 (tt0) REVERT: Cb 57 LYS cc_start: 0.8537 (ttmt) cc_final: 0.8283 (ttpp) REVERT: Cb 77 GLN cc_start: 0.7829 (tt0) cc_final: 0.7618 (tm-30) REVERT: Ea 512 TYR cc_start: 0.7797 (OUTLIER) cc_final: 0.6475 (t80) outliers start: 23 outliers final: 15 residues processed: 108 average time/residue: 0.1152 time to fit residues: 18.4548 Evaluate side-chains 108 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ca residue 77 GLN Chi-restraints excluded: chain Ca residue 119 THR 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 Bb residue 50 HIS Chi-restraints excluded: chain Da residue 60 LYS Chi-restraints excluded: chain Da residue 85 MET Chi-restraints excluded: chain Cb residue 119 THR Chi-restraints excluded: chain Ea residue 452 VAL Chi-restraints excluded: chain Ea residue 483 VAL Chi-restraints excluded: chain Ea residue 512 TYR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 72 optimal weight: 0.3980 chunk 102 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Bb 50 HIS ** Ea 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Fa 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.169135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.118002 restraints weight = 18176.534| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.02 r_work: 0.2968 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 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 = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15284 Z= 0.162 Angle : 0.528 5.595 21975 Z= 0.306 Chirality : 0.040 0.339 2551 Planarity : 0.005 0.082 1789 Dihedral : 29.510 176.412 4415 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.36 % Allowed : 26.62 % Favored : 71.02 % 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 are not related in a simple way. whole: 0.50 (0.26), residues: 1123 helix: 1.92 (0.21), residues: 639 sheet: 0.41 (0.84), residues: 42 loop : -2.24 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGEa 423 TYR 0.010 0.001 TYRDa 52 PHE 0.013 0.002 PHECa 79 TRP 0.007 0.001 TRPEb 752 HIS 0.005 0.001 HISBb 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (15284) covalent geometry : angle 0.52814 / 0.31 (21975) hydrogen bonds : bond 0.06809 / 7.75 ( 509) hydrogen bonds : angle 2.91015 / 3.74 ( 1417) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3150.73 seconds wall clock time: 54 minutes 18.34 seconds (3258.34 seconds total)