Starting phenix.real_space_refine on Tue Oct 27 11:12:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9npy_49636/10_2026/9npy_49636.cif Found real_map, /net/cci-nas-00/data/ceres_data/9npy_49636/10_2026/9npy_49636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9npy_49636/10_2026/9npy_49636.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9npy_49636/10_2026/9npy_49636.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9npy_49636/10_2026/9npy_49636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9npy_49636/10_2026/9npy_49636.map" } resolution = 2.1 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= 0.000 sd= 0.006 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: 8 Type Number sf(0) Gaussians K 9 8.98 5 Zn 2 6.06 5 P 483 5.49 5 Mg 21 5.21 5 S 69 5.16 5 C 13513 2.51 5 N 4451 2.21 5 O 6623 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25171 Number of models: 1 Model: "" Number of chains: 36 Chain: "B" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1601 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 10, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'GLU:plan': 11, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "J" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 776 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 88} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "L" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 634 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 1, 'TRANS': 106} Chain breaks: 1 Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 7, 'GLN:plan1': 4, 'GLU:plan': 7, 'HIS:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'TYR:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 120 Chain: "O" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 953 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 7, 'TRANS': 116} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 34 Chain: "Q" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1095 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 134} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "R" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 543 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 67} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "S" Number of atoms: 1072 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 140, 1070 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 3, 'TRANS': 136} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Conformer: "B" Number of residues, atoms: 140, 1070 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 3, 'TRANS': 136} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 1084 Chain: "T" Number of atoms: 1063 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 141, 1054 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 4, 'NMM:plan-2': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 141, 1054 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 4, 'NMM:plan-2': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 1061 Chain: "U" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 712 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 94} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 45 Chain: "Y" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 537 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 68} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "b" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 427 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "c" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 441 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 59} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 37 Chain: "d" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 450 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "i" Number of atoms: 10307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 10307 Classifications: {'RNA': 477, 'RNAv2': 6} Modifications used: {'rna2p': 1, 'rna2p_pur': 44, 'rna2p_pyr': 38, 'rna3p': 16, 'rna3p_pur': 192, 'rna3p_pyr': 190} Link IDs: {'rna2p': 83, 'rna3p': 399} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 1429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1429 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 177} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "g" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2272 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 10, 'TRANS': 296} Chain breaks: 1 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 74 Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "i" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Unusual residues: {' K': 7, ' MG': 19} Classifications: {'undetermined': 26} Link IDs: {None: 25} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "J" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "O" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "Q" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "R" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "S" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "T" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "U" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "i" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 634 Classifications: {'water': 634} Link IDs: {None: 633} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "g" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9204 SG CYS b 121 48.834 137.137 68.206 1.00153.16 S ATOM 9232 SG CYS b 126 51.652 135.328 66.301 1.00151.97 S ATOM 9345 SG CYS b 141 48.189 135.612 64.883 1.00137.23 S ATOM 9364 SG CYS b 144 48.910 133.316 67.881 1.00142.00 S ATOM 10012 SG CYS d 21 63.666 91.030 55.727 1.00 64.57 S ATOM 10036 SG CYS d 24 61.804 91.304 52.472 1.00 68.46 S ATOM 10157 SG CYS d 39 62.079 87.874 54.107 1.00 66.90 S ATOM 10183 SG CYS d 42 65.025 89.203 52.595 1.00 73.30 S Time building chain proxies: 5.18, per 1000 atoms: 0.21 Number of scatterers: 25171 At special positions: 0 Unit cell: (140.93, 167.458, 135.956, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 K 9 19.00 S 69 16.00 P 483 15.00 Mg 21 11.99 O 6623 8.00 N 4451 7.00 C 13513 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: 2.35 Conformation dependent library (CDL) restraints added in 815.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN b 201 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 141 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 126 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 121 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 144 " pdb=" ZN d 101 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 39 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 24 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 42 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 21 " Number of angles added : 12 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3484 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 25 sheets defined 41.6% alpha, 20.1% beta 134 base pairs and 236 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain 'B' and resid 6 through 29 Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 54 through 60 removed outlier: 3.530A pdb=" N VAL B 58 " --> pdb=" O ARG B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 78 Processing helix chain 'B' and resid 93 through 96 Processing helix chain 'B' and resid 97 through 111 Processing helix chain 'B' and resid 114 through 129 Processing helix chain 'B' and resid 162 through 167 removed outlier: 4.261A pdb=" N TYR B 166 " --> pdb=" O ASP B 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 19 Processing helix chain 'J' and resid 32 through 39 removed outlier: 3.844A pdb=" N ALA J 36 " --> pdb=" O PRO J 33 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ASP J 37 " --> pdb=" O GLU J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 55 Processing helix chain 'J' and resid 72 through 84 Processing helix chain 'J' and resid 91 through 96 Processing helix chain 'L' and resid 13 through 28 Processing helix chain 'L' and resid 34 through 44 Processing helix chain 'L' and resid 58 through 73 removed outlier: 3.555A pdb=" N VAL L 62 " --> pdb=" O GLU L 58 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 90 Processing helix chain 'L' and resid 118 through 128 Processing helix chain 'O' and resid 22 through 28 Processing helix chain 'O' and resid 29 through 37 removed outlier: 3.924A pdb=" N GLN O 35 " --> pdb=" O GLU O 31 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU O 36 " --> pdb=" O GLN O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 38 through 48 Processing helix chain 'O' and resid 50 through 67 Processing helix chain 'O' and resid 86 through 90 Processing helix chain 'O' and resid 108 through 112 Processing helix chain 'O' and resid 115 through 120 Processing helix chain 'Q' and resid 40 through 42 No H-bonds generated for 'chain 'Q' and resid 40 through 42' Processing helix chain 'Q' and resid 44 through 46 No H-bonds generated for 'chain 'Q' and resid 44 through 46' Processing helix chain 'Q' and resid 47 through 59 removed outlier: 3.566A pdb=" N LEU Q 51 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Proline residue: Q 54 - end of helix Processing helix chain 'Q' and resid 59 through 64 removed outlier: 4.094A pdb=" N PHE Q 63 " --> pdb=" O GLY Q 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 100 Processing helix chain 'Q' and resid 101 through 116 removed outlier: 3.691A pdb=" N LYS Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 117 through 120 Processing helix chain 'R' and resid 6 through 20 Processing helix chain 'R' and resid 21 through 24 Processing helix chain 'R' and resid 27 through 38 Processing helix chain 'R' and resid 43 through 64 Processing helix chain 'S' and resid 25 through 30 Processing helix chain 'S' and resid 31 through 33 No H-bonds generated for 'chain 'S' and resid 31 through 33' Processing helix chain 'S' and resid 37 through 48 Processing helix chain 'S' and resid 55 through 59 Processing helix chain 'S' and resid 60 through 73 Processing helix chain 'S' and resid 74 through 78 removed outlier: 3.539A pdb=" N LYS S 78 " --> pdb=" O ARG S 75 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 84 Processing helix chain 'S' and resid 100 through 117 Processing helix chain 'S' and resid 119 through 128 Processing helix chain 'T' and resid 5 through 9 Processing helix chain 'T' and resid 10 through 26 Processing helix chain 'T' and resid 51 through 67 removed outlier: 3.701A pdb=" N THR T 55 " --> pdb=" O ASN T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 71 through 79 Processing helix chain 'T' and resid 96 through 110 Processing helix chain 'T' and resid 124 through 143 Processing helix chain 'U' and resid 28 through 46 Processing helix chain 'U' and resid 94 through 103 Processing helix chain 'Y' and resid 51 through 62 Processing helix chain 'Y' and resid 63 through 65 No H-bonds generated for 'chain 'Y' and resid 63 through 65' Processing helix chain 'Y' and resid 69 through 78 Processing helix chain 'Y' and resid 80 through 95 Processing helix chain 'b' and resid 100 through 104 Processing helix chain 'd' and resid 3 through 7 Processing helix chain 'd' and resid 15 through 19 Processing helix chain 'd' and resid 32 through 36 Processing helix chain 'd' and resid 40 through 51 removed outlier: 5.380A pdb=" N LYS d 48 " --> pdb=" O ARG d 44 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ASP d 49 " --> pdb=" O GLN d 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 22 Processing helix chain 'E' and resid 42 through 46 Processing helix chain 'E' and resid 61 through 66 Processing helix chain 'E' and resid 67 through 76 Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'E' and resid 85 through 105 Processing helix chain 'E' and resid 107 through 120 Processing helix chain 'E' and resid 142 through 163 Processing helix chain 'E' and resid 168 through 183 Processing helix chain 'E' and resid 187 through 203 Processing sheet with id=AA1, first strand: chain 'B' and resid 34 through 40 removed outlier: 3.674A pdb=" N GLY B 36 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N THR B 46 " --> pdb=" O GLU B 85 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N TYR B 87 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE B 48 " --> pdb=" O TYR B 87 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLU B 89 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ILE B 50 " --> pdb=" O GLU B 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 148 through 155 removed outlier: 3.676A pdb=" N GLY B 133 " --> pdb=" O MET B 189 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 209 through 210 Processing sheet with id=AA4, first strand: chain 'B' and resid 224 through 226 removed outlier: 6.287A pdb=" N LEU g 184 " --> pdb=" O ASN g 178 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ASN g 178 " --> pdb=" O LEU g 184 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR g 186 " --> pdb=" O VAL g 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 20 through 23 Processing sheet with id=AA6, first strand: chain 'L' and resid 31 through 33 removed outlier: 3.712A pdb=" N LEU L 49 " --> pdb=" O VAL L 111 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'O' and resid 16 through 17 Processing sheet with id=AA8, first strand: chain 'O' and resid 76 through 78 Processing sheet with id=AA9, first strand: chain 'Q' and resid 9 through 16 removed outlier: 6.542A pdb=" N LYS Q 33 " --> pdb=" O VAL Q 70 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL Q 72 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 12 through 14 Processing sheet with id=AB2, first strand: chain 'T' and resid 81 through 85 removed outlier: 4.338A pdb=" N ASN T 85 " --> pdb=" O PRO T 89 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 113 through 115 Processing sheet with id=AB4, first strand: chain 'U' and resid 50 through 55 removed outlier: 6.716A pdb=" N VAL U 50 " --> pdb=" O HIS U 92 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N HIS U 92 " --> pdb=" O VAL U 50 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N GLY U 52 " --> pdb=" O ASP U 90 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ASP U 90 " --> pdb=" O GLY U 52 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'U' and resid 50 through 55 removed outlier: 6.716A pdb=" N VAL U 50 " --> pdb=" O HIS U 92 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N HIS U 92 " --> pdb=" O VAL U 50 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N GLY U 52 " --> pdb=" O ASP U 90 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ASP U 90 " --> pdb=" O GLY U 52 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Y' and resid 97 through 101 removed outlier: 6.629A pdb=" N ILE Y 108 " --> pdb=" O VAL Y 100 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'b' and resid 106 through 107 Processing sheet with id=AB8, first strand: chain 'b' and resid 133 through 134 Processing sheet with id=AB9, first strand: chain 'c' and resid 55 through 58 removed outlier: 6.603A pdb=" N THR c 15 " --> pdb=" O GLU c 33 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N GLU c 33 " --> pdb=" O THR c 15 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL c 17 " --> pdb=" O ARG c 31 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG c 31 " --> pdb=" O VAL c 17 " (cutoff:3.500A) removed outlier: 11.687A pdb=" N ALA E 138 " --> pdb=" O ILE c 43 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ASN c 45 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'd' and resid 30 through 31 Processing sheet with id=AC2, first strand: chain 'g' and resid 4 through 11 removed outlier: 6.707A pdb=" N VAL g 309 " --> pdb=" O ARG g 8 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR g 10 " --> pdb=" O VAL g 307 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL g 307 " --> pdb=" O THR g 10 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER g 288 " --> pdb=" O GLY g 301 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'g' and resid 18 through 23 removed outlier: 3.725A pdb=" N GLN g 20 " --> pdb=" O ALA g 34 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LYS g 44 " --> pdb=" O PRO g 55 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'g' and resid 66 through 71 removed outlier: 3.760A pdb=" N ASP g 68 " --> pdb=" O GLY g 81 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU g 87 " --> pdb=" O ARG g 100 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ARG g 100 " --> pdb=" O LEU g 87 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU g 89 " --> pdb=" O THR g 98 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR g 96 " --> pdb=" O ASP g 91 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'g' and resid 108 through 113 Processing sheet with id=AC6, first strand: chain 'g' and resid 195 through 200 removed outlier: 4.597A pdb=" N GLY g 211 " --> pdb=" O GLN g 215 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N GLN g 215 " --> pdb=" O GLY g 211 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR g 228 " --> pdb=" O LEU g 218 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ASP g 220 " --> pdb=" O HIS g 226 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N HIS g 226 " --> pdb=" O ASP g 220 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'g' and resid 236 through 241 removed outlier: 6.503A pdb=" N ALA g 251 " --> pdb=" O ASN g 237 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU g 239 " --> pdb=" O CYS g 249 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N CYS g 249 " --> pdb=" O LEU g 239 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N PHE g 241 " --> pdb=" O TRP g 247 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N TRP g 247 " --> pdb=" O PHE g 241 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE g 256 " --> pdb=" O GLU g 269 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU g 269 " --> pdb=" O ILE g 256 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ILE g 258 " --> pdb=" O VAL g 267 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE g 265 " --> pdb=" O ASP g 260 " (cutoff:3.500A) 716 hydrogen bonds defined for protein. 1976 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 335 hydrogen bonds 518 hydrogen bond angles 0 basepair planarities 134 basepair parallelities 236 stacking parallelities Total time for adding SS restraints: 10.24 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2686 1.29 - 1.42: 9480 1.42 - 1.55: 12519 1.55 - 1.68: 971 1.68 - 1.81: 106 Bond restraints: 25762 Sorted by residual: bond pdb=" C5 4AC i1337 " pdb=" C6 4AC i1337 " ideal model delta sigma weight residual 1.356 1.492 -0.136 2.00e-02 2.50e+03 4.60e+01 bond pdb=" N3 4AC i1337 " pdb=" C4 4AC i1337 " ideal model delta sigma weight residual 1.307 1.442 -0.135 2.00e-02 2.50e+03 4.54e+01 bond pdb=" C2 4AC i1337 " pdb=" N3 4AC i1337 " ideal model delta sigma weight residual 1.348 1.478 -0.130 2.00e-02 2.50e+03 4.26e+01 bond pdb=" C2 PSU i1244 " pdb=" N3 PSU i1244 " ideal model delta sigma weight residual 1.380 1.507 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" C2 PSU i1367 " pdb=" N3 PSU i1367 " ideal model delta sigma weight residual 1.380 1.506 -0.126 2.00e-02 2.50e+03 3.98e+01 ... (remaining 25757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 35880 2.22 - 4.43: 1199 4.43 - 6.65: 60 6.65 - 8.86: 24 8.86 - 11.08: 10 Bond angle restraints: 37173 Sorted by residual: angle pdb=" C1' C i1453 " pdb=" N1 C i1453 " pdb=" C2 C i1453 " ideal model delta sigma weight residual 118.80 126.24 -7.44 1.10e+00 8.26e-01 4.58e+01 angle pdb=" C5 G i1520 " pdb=" C4 G i1520 " pdb=" N3 G i1520 " ideal model delta sigma weight residual 128.60 125.54 3.06 5.00e-01 4.00e+00 3.74e+01 angle pdb=" N1 C i1453 " pdb=" C2 C i1453 " pdb=" O2 C i1453 " ideal model delta sigma weight residual 118.90 122.56 -3.66 6.00e-01 2.78e+00 3.72e+01 angle pdb=" C2 G i1520 " pdb=" N3 G i1520 " pdb=" C4 G i1520 " ideal model delta sigma weight residual 111.90 114.75 -2.85 5.00e-01 4.00e+00 3.24e+01 angle pdb=" O5' C i1521 " pdb=" C5' C i1521 " pdb=" C4' C i1521 " ideal model delta sigma weight residual 109.40 113.29 -3.89 8.00e-01 1.56e+00 2.36e+01 ... (remaining 37168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 15006 35.58 - 71.16: 1043 71.16 - 106.75: 189 106.75 - 142.33: 4 142.33 - 177.91: 8 Dihedral angle restraints: 16250 sinusoidal: 10847 harmonic: 5403 Sorted by residual: dihedral pdb=" O4' U i1315 " pdb=" C1' U i1315 " pdb=" N1 U i1315 " pdb=" C2 U i1315 " ideal model delta sinusoidal sigma weight residual -160.00 -15.23 -144.77 1 1.50e+01 4.44e-03 7.75e+01 dihedral pdb=" O4' U i1314 " pdb=" C1' U i1314 " pdb=" N1 U i1314 " pdb=" C2 U i1314 " ideal model delta sinusoidal sigma weight residual 200.00 59.35 140.65 1 1.50e+01 4.44e-03 7.57e+01 dihedral pdb=" O4' C i1423 " pdb=" C1' C i1423 " pdb=" N1 C i1423 " pdb=" C2 C i1423 " ideal model delta sinusoidal sigma weight residual -128.00 49.91 -177.91 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 16247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3819 0.075 - 0.150: 783 0.150 - 0.225: 21 0.225 - 0.299: 8 0.299 - 0.374: 3 Chirality restraints: 4634 Sorted by residual: chirality pdb=" C3' A2M i1383 " pdb=" C4' A2M i1383 " pdb=" O3' A2M i1383 " pdb=" C2' A2M i1383 " both_signs ideal model delta sigma weight residual False -2.74 -2.36 -0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" C3' A2M i1678 " pdb=" C4' A2M i1678 " pdb=" O3' A2M i1678 " pdb=" C2' A2M i1678 " both_signs ideal model delta sigma weight residual False -2.74 -2.37 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" C1' A2M i1678 " pdb=" O4' A2M i1678 " pdb=" C2' A2M i1678 " pdb=" N9 A2M i1678 " both_signs ideal model delta sigma weight residual False 2.28 1.98 0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 4631 not shown) Planarity restraints: 2927 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A i1240 " 0.041 2.00e-02 2.50e+03 1.86e-02 9.47e+00 pdb=" N9 A i1240 " -0.043 2.00e-02 2.50e+03 pdb=" C8 A i1240 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A i1240 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A i1240 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A i1240 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A i1240 " 0.011 2.00e-02 2.50e+03 pdb=" N1 A i1240 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A i1240 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A i1240 " -0.007 2.00e-02 2.50e+03 pdb=" C4 A i1240 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G i1606 " 0.041 2.00e-02 2.50e+03 1.73e-02 8.96e+00 pdb=" N9 G i1606 " -0.040 2.00e-02 2.50e+03 pdb=" C8 G i1606 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G i1606 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G i1606 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G i1606 " 0.010 2.00e-02 2.50e+03 pdb=" O6 G i1606 " 0.009 2.00e-02 2.50e+03 pdb=" N1 G i1606 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G i1606 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G i1606 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G i1606 " -0.009 2.00e-02 2.50e+03 pdb=" C4 G i1606 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G i1605 " -0.033 2.00e-02 2.50e+03 1.39e-02 5.76e+00 pdb=" N9 G i1605 " 0.032 2.00e-02 2.50e+03 pdb=" C8 G i1605 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G i1605 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G i1605 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G i1605 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G i1605 " -0.011 2.00e-02 2.50e+03 pdb=" N1 G i1605 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G i1605 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G i1605 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G i1605 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G i1605 " 0.003 2.00e-02 2.50e+03 ... (remaining 2924 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.49: 395 2.49 - 3.15: 19882 3.15 - 3.81: 57887 3.81 - 4.48: 84635 4.48 - 5.14: 118628 Nonbonded interactions: 281427 Sorted by model distance: nonbonded pdb="MG MG i1905 " pdb=" O HOH i2318 " model vdw 1.823 2.170 nonbonded pdb="MG MG i1909 " pdb=" O HOH i2008 " model vdw 1.831 2.170 nonbonded pdb="MG MG i1911 " pdb=" O HOH i2360 " model vdw 1.835 2.170 nonbonded pdb="MG MG i1911 " pdb=" O HOH i2014 " model vdw 1.835 2.170 nonbonded pdb="MG MG i1907 " pdb=" O HOH i2202 " model vdw 1.838 2.170 ... (remaining 281422 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.42 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: 8.870 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: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 33.020 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9224 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.136 25770 Z= 0.460 Angle : 0.774 11.079 37185 Z= 0.545 Chirality : 0.057 0.374 4634 Planarity : 0.004 0.052 2927 Dihedral : 20.700 177.912 12766 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.97 % Allowed : 4.32 % Favored : 94.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.06 % 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: 1.54 (0.19), residues: 1836 helix: 2.34 (0.20), residues: 662 sheet: 0.42 (0.26), residues: 359 loop : 0.30 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 5 TYR 0.013 0.001 TYR B 107 PHE 0.022 0.002 PHE J 67 TRP 0.014 0.001 TRP g 132 HIS 0.004 0.001 HIS T 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00681 / 0.46 (25762) covalent geometry : angle 0.77180 / 0.54 (37173) hydrogen bonds : bond 0.06272 / 4.25 ( 1049) hydrogen bonds : angle 4.10226 / 2.99 ( 2494) metal coordination : bond 0.00780 / 0.52 ( 8) metal coordination : angle 3.51852 / 1.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 274 time to evaluate : 0.471 Fit side-chains REVERT: L 121 LYS cc_start: 0.8454 (tttp) cc_final: 0.7919 (ttmt) REVERT: O 24 GLN cc_start: 0.8747 (mt0) cc_final: 0.8255 (mt0) REVERT: O 52 LYS cc_start: 0.8819 (mtmt) cc_final: 0.8436 (mttt) REVERT: O 82 ASP cc_start: 0.9208 (p0) cc_final: 0.8924 (p0) REVERT: R 19 LYS cc_start: 0.9177 (mttm) cc_final: 0.8965 (mttt) REVERT: R 58 MET cc_start: 0.9442 (mmm) cc_final: 0.9170 (mmm) REVERT: S 21 ASP cc_start: 0.8645 (t0) cc_final: 0.8337 (t0) REVERT: c 10 LYS cc_start: 0.8953 (tppp) cc_final: 0.8571 (mmtt) REVERT: E 136 ARG cc_start: 0.8549 (mtt-85) cc_final: 0.8231 (mtt-85) REVERT: g 187 ASN cc_start: 0.8562 (t0) cc_final: 0.8141 (t0) REVERT: g 189 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8690 (mp) REVERT: g 222 ASN cc_start: 0.9189 (m110) cc_final: 0.8971 (m110) outliers start: 13 outliers final: 5 residues processed: 285 average time/residue: 0.6748 time to fit residues: 220.6687 Evaluate side-chains 260 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 254 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain g residue 189 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 200] chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 0.9980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 74 GLN J 66 HIS O 24 GLN O 104 GLN Q 8 GLN S 72 GLN U 81 GLN c 29 GLN E 29 GLN E 83 ASN g 15 ASN g 117 ASN g 272 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.066728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.048780 restraints weight = 63999.269| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 1.43 r_work: 0.2557 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2453 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2453 r_free = 0.2453 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2453 r_free = 0.2453 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2453 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9236 moved from start: 0.0597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 25770 Z= 0.252 Angle : 0.605 11.658 37185 Z= 0.324 Chirality : 0.045 0.389 4634 Planarity : 0.005 0.049 2927 Dihedral : 22.233 178.745 9715 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.64 % Allowed : 9.09 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.06 % 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: 1.42 (0.19), residues: 1836 helix: 2.22 (0.20), residues: 660 sheet: 0.37 (0.26), residues: 354 loop : 0.24 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 129 TYR 0.021 0.002 TYR B 107 PHE 0.024 0.002 PHE J 67 TRP 0.012 0.001 TRP g 132 HIS 0.004 0.001 HIS R 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.25 (25762) covalent geometry : angle 0.60137 / 0.32 (37173) hydrogen bonds : bond 0.05615 / 3.83 ( 1049) hydrogen bonds : angle 3.89087 / 2.82 ( 2494) metal coordination : bond 0.00880 / 0.59 ( 8) metal coordination : angle 3.57715 / 2.01 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 256 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 193 ASP cc_start: 0.8964 (t0) cc_final: 0.8495 (t0) REVERT: L 121 LYS cc_start: 0.8509 (tttp) cc_final: 0.7955 (ttmt) REVERT: O 50 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7258 (mpt180) REVERT: O 52 LYS cc_start: 0.8846 (mtmt) cc_final: 0.8451 (mttt) REVERT: O 82 ASP cc_start: 0.9258 (p0) cc_final: 0.8986 (p0) REVERT: O 106 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8587 (tt0) REVERT: R 5 ARG cc_start: 0.9275 (OUTLIER) cc_final: 0.8454 (mtt180) REVERT: R 19 LYS cc_start: 0.9176 (mttm) cc_final: 0.8948 (mttt) REVERT: R 58 MET cc_start: 0.9436 (mmm) cc_final: 0.9150 (mmm) REVERT: S 21 ASP cc_start: 0.8678 (t0) cc_final: 0.8368 (t0) REVERT: c 10 LYS cc_start: 0.8948 (tppp) cc_final: 0.8573 (mmtt) REVERT: E 136 ARG cc_start: 0.8688 (mtt-85) cc_final: 0.8312 (mtt-85) REVERT: g 187 ASN cc_start: 0.8547 (t0) cc_final: 0.8133 (t0) REVERT: g 189 ILE cc_start: 0.8983 (mt) cc_final: 0.8649 (mp) REVERT: g 222 ASN cc_start: 0.9215 (m110) cc_final: 0.9006 (m110) outliers start: 22 outliers final: 4 residues processed: 269 average time/residue: 0.6862 time to fit residues: 211.6046 Evaluate side-chains 259 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 252 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain O residue 50 ARG Chi-restraints excluded: chain O residue 106 GLU Chi-restraints excluded: chain R residue 5 ARG Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain g residue 132 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: [154, 85, 103, 146, 25, 187, 72, 77, 11, 32, 157] chunk 154 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 146 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 77 optimal weight: 0.2980 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 157 optimal weight: 20.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 104 GLN S 72 GLN g 15 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.068983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.051269 restraints weight = 64172.835| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 1.44 r_work: 0.2632 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2528 r_free = 0.2528 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2528 r_free = 0.2528 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9193 moved from start: 0.0814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25770 Z= 0.125 Angle : 0.524 11.408 37185 Z= 0.284 Chirality : 0.039 0.356 4634 Planarity : 0.004 0.049 2927 Dihedral : 22.110 179.280 9709 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.09 % Allowed : 9.61 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.06 % 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: 1.56 (0.19), residues: 1836 helix: 2.40 (0.20), residues: 661 sheet: 0.43 (0.26), residues: 353 loop : 0.27 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 129 TYR 0.015 0.001 TYR g 246 PHE 0.018 0.001 PHE J 67 TRP 0.014 0.001 TRP g 132 HIS 0.004 0.001 HIS T 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.13 (25762) covalent geometry : angle 0.52085 / 0.28 (37173) hydrogen bonds : bond 0.05026 / 3.37 ( 1049) hydrogen bonds : angle 3.72516 / 2.69 ( 2494) metal coordination : bond 0.00520 / 0.32 ( 8) metal coordination : angle 3.20068 / 1.77 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 266 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: B 193 ASP cc_start: 0.8994 (t0) cc_final: 0.8544 (t0) REVERT: J 17 LYS cc_start: 0.9392 (OUTLIER) cc_final: 0.9105 (tttp) REVERT: L 37 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7961 (mt-10) REVERT: L 121 LYS cc_start: 0.8484 (tttp) cc_final: 0.7918 (ttmt) REVERT: O 21 ASP cc_start: 0.8424 (p0) cc_final: 0.7986 (p0) REVERT: O 24 GLN cc_start: 0.8985 (mt0) cc_final: 0.8636 (mt0) REVERT: O 50 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7307 (mpt180) REVERT: O 52 LYS cc_start: 0.8827 (mtmt) cc_final: 0.8462 (mttt) REVERT: O 82 ASP cc_start: 0.9201 (p0) cc_final: 0.8944 (p0) REVERT: O 101 THR cc_start: 0.9188 (m) cc_final: 0.8974 (p) REVERT: O 106 GLU cc_start: 0.8903 (tt0) cc_final: 0.8343 (tt0) REVERT: R 5 ARG cc_start: 0.9268 (OUTLIER) cc_final: 0.8446 (mtt180) REVERT: R 19 LYS cc_start: 0.9123 (mttm) cc_final: 0.8905 (mttt) REVERT: R 58 MET cc_start: 0.9395 (mmm) cc_final: 0.9137 (mmm) REVERT: S 21 ASP cc_start: 0.8683 (t0) cc_final: 0.8378 (t0) REVERT: c 10 LYS cc_start: 0.8958 (tppp) cc_final: 0.8598 (mmtt) REVERT: E 136 ARG cc_start: 0.8638 (mtt-85) cc_final: 0.8291 (mtt-85) REVERT: g 222 ASN cc_start: 0.9200 (m110) cc_final: 0.8985 (m110) outliers start: 28 outliers final: 12 residues processed: 278 average time/residue: 0.7102 time to fit residues: 225.3082 Evaluate side-chains 267 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 252 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain J residue 17 LYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 50 ARG Chi-restraints excluded: chain R residue 5 ARG Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain Y residue 89 GLN Chi-restraints excluded: chain c residue 52 GLU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain g residue 132 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: [36, 12, 166, 107, 171, 177, 74, 28, 55, 153, 34] chunk 36 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 166 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 153 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 32 GLN O 104 GLN S 72 GLN g 15 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.065640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.047877 restraints weight = 55222.502| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 1.35 r_work: 0.2538 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2435 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2435 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2435 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2435 r_free = 0.2435 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2435 r_free = 0.2435 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2435 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9251 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 25770 Z= 0.377 Angle : 0.681 11.283 37185 Z= 0.355 Chirality : 0.050 0.420 4634 Planarity : 0.005 0.054 2927 Dihedral : 22.124 178.659 9709 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.56 % Allowed : 10.66 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.06 % 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 (0.19), residues: 1836 helix: 2.15 (0.20), residues: 659 sheet: 0.22 (0.26), residues: 358 loop : 0.17 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG g 245 TYR 0.027 0.002 TYR B 107 PHE 0.028 0.002 PHE J 67 TRP 0.010 0.002 TRP S 82 HIS 0.005 0.001 HIS R 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00750 / 0.38 (25762) covalent geometry : angle 0.67761 / 0.35 (37173) hydrogen bonds : bond 0.06092 / 4.15 ( 1049) hydrogen bonds : angle 3.91777 / 2.83 ( 2494) metal coordination : bond 0.01043 / 0.70 ( 8) metal coordination : angle 3.57147 / 2.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 253 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: B 193 ASP cc_start: 0.8953 (t0) cc_final: 0.8475 (t0) REVERT: J 17 LYS cc_start: 0.9380 (OUTLIER) cc_final: 0.9087 (tttp) REVERT: L 52 LEU cc_start: 0.5499 (tt) cc_final: 0.5223 (tm) REVERT: L 121 LYS cc_start: 0.8506 (tttp) cc_final: 0.7938 (ttmt) REVERT: O 21 ASP cc_start: 0.8484 (p0) cc_final: 0.8014 (p0) REVERT: O 24 GLN cc_start: 0.9021 (mt0) cc_final: 0.8710 (mt0) REVERT: O 50 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7354 (mpt180) REVERT: O 52 LYS cc_start: 0.8885 (mtmt) cc_final: 0.8482 (mttt) REVERT: O 82 ASP cc_start: 0.9246 (p0) cc_final: 0.9012 (p0) REVERT: O 106 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8587 (tt0) REVERT: R 5 ARG cc_start: 0.9289 (OUTLIER) cc_final: 0.8531 (mtt180) REVERT: R 19 LYS cc_start: 0.9201 (mttm) cc_final: 0.8975 (mttt) REVERT: R 58 MET cc_start: 0.9428 (mmm) cc_final: 0.9195 (mmm) REVERT: S 21 ASP cc_start: 0.8666 (t0) cc_final: 0.8386 (t0) REVERT: c 10 LYS cc_start: 0.8988 (tppp) cc_final: 0.8627 (mmtt) REVERT: E 136 ARG cc_start: 0.8706 (mtt-85) cc_final: 0.8420 (mtt-85) REVERT: g 305 ASN cc_start: 0.9301 (OUTLIER) cc_final: 0.9076 (m-40) outliers start: 21 outliers final: 8 residues processed: 263 average time/residue: 0.6941 time to fit residues: 209.4371 Evaluate side-chains 264 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 251 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain J residue 17 LYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain O residue 50 ARG Chi-restraints excluded: chain O residue 106 GLU Chi-restraints excluded: chain R residue 5 ARG Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain c residue 52 GLU Chi-restraints excluded: chain g residue 305 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: [69, 72, 154, 74, 159, 215, 111, 193, 54, 67, 131] chunk 69 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 154 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 159 optimal weight: 10.0000 chunk 215 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 chunk 193 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 32 GLN O 104 GLN S 72 GLN g 15 ASN g 272 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.068697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.051217 restraints weight = 55029.924| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 1.33 r_work: 0.2636 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2532 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2532 r_free = 0.2532 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2532 r_free = 0.2532 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2532 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9195 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25770 Z= 0.125 Angle : 0.532 11.410 37185 Z= 0.289 Chirality : 0.039 0.362 4634 Planarity : 0.004 0.047 2927 Dihedral : 22.089 179.053 9709 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.64 % Allowed : 11.33 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.06 % 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: 1.58 (0.20), residues: 1836 helix: 2.46 (0.20), residues: 653 sheet: 0.34 (0.26), residues: 365 loop : 0.31 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG g 245 TYR 0.012 0.001 TYR L 61 PHE 0.017 0.001 PHE J 67 TRP 0.014 0.001 TRP g 132 HIS 0.004 0.001 HIS T 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (25762) covalent geometry : angle 0.52889 / 0.29 (37173) hydrogen bonds : bond 0.05051 / 3.39 ( 1049) hydrogen bonds : angle 3.72701 / 2.69 ( 2494) metal coordination : bond 0.00548 / 0.34 ( 8) metal coordination : angle 3.22644 / 1.78 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 254 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: B 193 ASP cc_start: 0.8962 (t0) cc_final: 0.8508 (t0) REVERT: J 17 LYS cc_start: 0.9383 (OUTLIER) cc_final: 0.9104 (tttp) REVERT: J 38 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8209 (mptp) REVERT: L 121 LYS cc_start: 0.8480 (tttp) cc_final: 0.7898 (ttmt) REVERT: O 21 ASP cc_start: 0.8452 (p0) cc_final: 0.8004 (p0) REVERT: O 24 GLN cc_start: 0.9026 (mt0) cc_final: 0.8700 (mt0) REVERT: O 50 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7334 (mpt180) REVERT: O 52 LYS cc_start: 0.8848 (mtmt) cc_final: 0.8466 (mttt) REVERT: O 82 ASP cc_start: 0.9206 (p0) cc_final: 0.8974 (p0) REVERT: O 101 THR cc_start: 0.9193 (m) cc_final: 0.8949 (p) REVERT: O 106 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8309 (tt0) REVERT: R 5 ARG cc_start: 0.9271 (OUTLIER) cc_final: 0.8474 (mtt180) REVERT: R 19 LYS cc_start: 0.9125 (mttm) cc_final: 0.8901 (mttt) REVERT: R 58 MET cc_start: 0.9382 (mmm) cc_final: 0.9108 (mmm) REVERT: S 21 ASP cc_start: 0.8690 (t0) cc_final: 0.8362 (t0) REVERT: c 10 LYS cc_start: 0.8942 (tppp) cc_final: 0.8632 (tptp) REVERT: E 136 ARG cc_start: 0.8652 (mtt-85) cc_final: 0.8378 (mtt-85) REVERT: g 296 GLN cc_start: 0.9109 (mm110) cc_final: 0.8777 (mp-120) outliers start: 22 outliers final: 10 residues processed: 264 average time/residue: 0.7028 time to fit residues: 212.3141 Evaluate side-chains 265 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 250 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 17 LYS Chi-restraints excluded: chain J residue 38 LYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 50 ARG Chi-restraints excluded: chain O residue 106 GLU Chi-restraints excluded: chain R residue 5 ARG Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain Y residue 89 GLN Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain g residue 132 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: [38, 225, 55, 230, 107, 104, 169, 141, 205, 72, 170] chunk 38 optimal weight: 10.0000 chunk 225 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 230 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 169 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 205 optimal weight: 0.0980 chunk 72 optimal weight: 1.9990 chunk 170 optimal weight: 10.0000 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 32 GLN O 104 GLN S 72 GLN g 15 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.067047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.049333 restraints weight = 54383.395| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 1.32 r_work: 0.2581 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2480 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2480 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2480 r_free = 0.2480 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2480 r_free = 0.2480 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2480 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9227 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25770 Z= 0.224 Angle : 0.578 11.290 37185 Z= 0.308 Chirality : 0.043 0.392 4634 Planarity : 0.004 0.049 2927 Dihedral : 22.030 178.426 9709 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.64 % Allowed : 12.00 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.06 % 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: 1.48 (0.19), residues: 1836 helix: 2.35 (0.20), residues: 660 sheet: 0.32 (0.26), residues: 355 loop : 0.24 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 104 TYR 0.022 0.001 TYR B 107 PHE 0.023 0.002 PHE J 67 TRP 0.011 0.001 TRP g 132 HIS 0.004 0.001 HIS R 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.22 (25762) covalent geometry : angle 0.57503 / 0.31 (37173) hydrogen bonds : bond 0.05372 / 3.63 ( 1049) hydrogen bonds : angle 3.75083 / 2.71 ( 2494) metal coordination : bond 0.00724 / 0.48 ( 8) metal coordination : angle 3.28069 / 1.84 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 254 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: B 193 ASP cc_start: 0.8968 (t0) cc_final: 0.8498 (t0) REVERT: J 38 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8282 (mptp) REVERT: L 121 LYS cc_start: 0.8481 (tttp) cc_final: 0.7916 (ttmt) REVERT: O 21 ASP cc_start: 0.8483 (p0) cc_final: 0.8023 (p0) REVERT: O 24 GLN cc_start: 0.9049 (mt0) cc_final: 0.8740 (mt0) REVERT: O 50 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7278 (mpt180) REVERT: O 52 LYS cc_start: 0.8865 (mtmt) cc_final: 0.8454 (mttt) REVERT: O 82 ASP cc_start: 0.9224 (p0) cc_final: 0.8960 (p0) REVERT: O 101 THR cc_start: 0.9237 (m) cc_final: 0.9014 (p) REVERT: O 106 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8561 (tt0) REVERT: R 5 ARG cc_start: 0.9274 (OUTLIER) cc_final: 0.8470 (mtt180) REVERT: S 21 ASP cc_start: 0.8702 (t0) cc_final: 0.8386 (t0) REVERT: c 10 LYS cc_start: 0.8988 (tppp) cc_final: 0.8688 (tptp) REVERT: E 43 GLU cc_start: 0.8406 (mp0) cc_final: 0.8177 (mp0) REVERT: E 136 ARG cc_start: 0.8679 (mtt-85) cc_final: 0.8402 (mtt-85) outliers start: 22 outliers final: 12 residues processed: 263 average time/residue: 0.6983 time to fit residues: 209.9389 Evaluate side-chains 268 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 252 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain J residue 38 LYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 50 ARG Chi-restraints excluded: chain O residue 106 GLU Chi-restraints excluded: chain R residue 5 ARG Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 34 LYS Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain Y residue 89 GLN Chi-restraints excluded: chain c residue 52 GLU Chi-restraints excluded: chain E residue 185 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: [228, 168, 33, 176, 229, 160, 132, 225, 91, 96, 127] chunk 228 optimal weight: 2.9990 chunk 168 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 176 optimal weight: 10.0000 chunk 229 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 225 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 127 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 32 GLN O 104 GLN S 72 GLN g 15 ASN g 272 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.066468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.048265 restraints weight = 73782.148| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 1.53 r_work: 0.2543 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2438 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2437 r_free = 0.2437 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2437 r_free = 0.2437 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9243 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 25770 Z= 0.264 Angle : 0.615 11.358 37185 Z= 0.325 Chirality : 0.045 0.398 4634 Planarity : 0.005 0.049 2927 Dihedral : 22.053 178.459 9709 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.71 % Allowed : 12.00 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.06 % 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: 1.37 (0.19), residues: 1836 helix: 2.27 (0.20), residues: 660 sheet: 0.19 (0.26), residues: 355 loop : 0.20 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 104 TYR 0.015 0.002 TYR B 107 PHE 0.024 0.002 PHE J 67 TRP 0.011 0.001 TRP g 132 HIS 0.005 0.001 HIS R 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.26 (25762) covalent geometry : angle 0.61167 / 0.33 (37173) hydrogen bonds : bond 0.05622 / 3.82 ( 1049) hydrogen bonds : angle 3.82150 / 2.76 ( 2494) metal coordination : bond 0.00835 / 0.55 ( 8) metal coordination : angle 3.39739 / 1.92 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 253 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: B 193 ASP cc_start: 0.8967 (t0) cc_final: 0.8470 (t0) REVERT: J 38 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8308 (mptp) REVERT: L 121 LYS cc_start: 0.8440 (tttp) cc_final: 0.7860 (ttmt) REVERT: O 21 ASP cc_start: 0.8520 (p0) cc_final: 0.8061 (p0) REVERT: O 24 GLN cc_start: 0.9075 (mt0) cc_final: 0.8766 (mt0) REVERT: O 50 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7330 (mpt180) REVERT: O 52 LYS cc_start: 0.8894 (mtmt) cc_final: 0.8512 (mttt) REVERT: O 82 ASP cc_start: 0.9252 (p0) cc_final: 0.8990 (p0) REVERT: O 106 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8599 (tt0) REVERT: R 5 ARG cc_start: 0.9291 (OUTLIER) cc_final: 0.8515 (mtt180) REVERT: S 21 ASP cc_start: 0.8663 (t0) cc_final: 0.8371 (t0) REVERT: Y 44 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8423 (pp) REVERT: c 10 LYS cc_start: 0.9017 (tppp) cc_final: 0.8732 (tptp) REVERT: E 136 ARG cc_start: 0.8705 (mtt-85) cc_final: 0.8413 (mtt-85) outliers start: 23 outliers final: 11 residues processed: 262 average time/residue: 0.7139 time to fit residues: 214.1718 Evaluate side-chains 265 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 249 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 38 LYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 50 ARG Chi-restraints excluded: chain O residue 106 GLU Chi-restraints excluded: chain R residue 5 ARG Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 34 LYS Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Y residue 89 GLN Chi-restraints excluded: chain c residue 52 GLU Chi-restraints excluded: chain E residue 185 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: [225, 192, 141, 104, 15, 36, 213, 218, 113, 223, 105] chunk 225 optimal weight: 6.9990 chunk 192 optimal weight: 0.9980 chunk 141 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 36 optimal weight: 6.9990 chunk 213 optimal weight: 7.9990 chunk 218 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 223 optimal weight: 0.0770 chunk 105 optimal weight: 0.2980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 32 GLN O 104 GLN S 72 GLN g 15 ASN g 272 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.069662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.052004 restraints weight = 64013.540| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 1.46 r_work: 0.2657 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2556 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2556 r_free = 0.2556 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2556 r_free = 0.2556 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9176 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25770 Z= 0.109 Angle : 0.521 11.346 37185 Z= 0.283 Chirality : 0.038 0.345 4634 Planarity : 0.004 0.046 2927 Dihedral : 22.003 179.683 9709 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.64 % Allowed : 12.22 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.06 % 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: 1.62 (0.20), residues: 1836 helix: 2.50 (0.20), residues: 656 sheet: 0.34 (0.26), residues: 366 loop : 0.34 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Y 104 TYR 0.019 0.001 TYR E 188 PHE 0.015 0.001 PHE J 67 TRP 0.015 0.001 TRP g 132 HIS 0.003 0.001 HIS T 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.11 (25762) covalent geometry : angle 0.51761 / 0.28 (37173) hydrogen bonds : bond 0.04921 / 3.27 ( 1049) hydrogen bonds : angle 3.67038 / 2.65 ( 2494) metal coordination : bond 0.00444 / 0.28 ( 8) metal coordination : angle 3.14398 / 1.73 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 259 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 193 ASP cc_start: 0.8950 (t0) cc_final: 0.8510 (t0) REVERT: J 38 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8174 (mptp) REVERT: L 121 LYS cc_start: 0.8453 (tttp) cc_final: 0.7822 (ttmt) REVERT: O 50 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7315 (mpt180) REVERT: O 52 LYS cc_start: 0.8859 (mtmt) cc_final: 0.8465 (mttt) REVERT: O 82 ASP cc_start: 0.9200 (p0) cc_final: 0.8952 (p0) REVERT: O 101 THR cc_start: 0.9201 (m) cc_final: 0.8999 (p) REVERT: O 106 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8341 (tt0) REVERT: R 5 ARG cc_start: 0.9267 (OUTLIER) cc_final: 0.8419 (mtt180) REVERT: S 21 ASP cc_start: 0.8700 (t0) cc_final: 0.8351 (t0) REVERT: U 38 ASP cc_start: 0.8654 (m-30) cc_final: 0.8432 (m-30) REVERT: c 10 LYS cc_start: 0.8958 (tppp) cc_final: 0.8668 (tptp) REVERT: E 136 ARG cc_start: 0.8683 (mtt-85) cc_final: 0.8393 (mtt-85) REVERT: g 296 GLN cc_start: 0.9093 (mm110) cc_final: 0.8860 (mp-120) outliers start: 22 outliers final: 10 residues processed: 270 average time/residue: 0.6920 time to fit residues: 214.2635 Evaluate side-chains 263 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 249 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 38 LYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 50 ARG Chi-restraints excluded: chain O residue 106 GLU Chi-restraints excluded: chain R residue 5 ARG Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain Y residue 89 GLN Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain g residue 132 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: [196, 83, 126, 3, 79, 8, 40, 70, 222, 61, 116] chunk 196 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 3 optimal weight: 0.0030 chunk 79 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 70 optimal weight: 6.9990 chunk 222 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 overall best weight: 2.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 32 GLN O 104 GLN S 72 GLN g 15 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.067358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.049686 restraints weight = 54462.533| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 1.32 r_work: 0.2592 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2490 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2488 r_free = 0.2488 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2488 r_free = 0.2488 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9223 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25770 Z= 0.208 Angle : 0.578 11.225 37185 Z= 0.305 Chirality : 0.043 0.389 4634 Planarity : 0.004 0.048 2927 Dihedral : 21.952 178.398 9709 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.12 % Allowed : 13.04 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.06 % 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: 1.50 (0.19), residues: 1836 helix: 2.39 (0.20), residues: 662 sheet: 0.30 (0.26), residues: 357 loop : 0.24 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG c 13 TYR 0.022 0.001 TYR B 107 PHE 0.029 0.002 PHE b 136 TRP 0.010 0.001 TRP g 132 HIS 0.004 0.001 HIS R 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.21 (25762) covalent geometry : angle 0.57521 / 0.31 (37173) hydrogen bonds : bond 0.05261 / 3.54 ( 1049) hydrogen bonds : angle 3.71186 / 2.68 ( 2494) metal coordination : bond 0.00597 / 0.38 ( 8) metal coordination : angle 3.19905 / 1.79 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 251 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: B 193 ASP cc_start: 0.8962 (t0) cc_final: 0.8496 (t0) REVERT: J 38 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8220 (mptp) REVERT: L 121 LYS cc_start: 0.8449 (tttp) cc_final: 0.7853 (ttmt) REVERT: O 21 ASP cc_start: 0.8475 (p0) cc_final: 0.7973 (p0) REVERT: O 24 GLN cc_start: 0.9070 (mt0) cc_final: 0.8756 (mt0) REVERT: O 50 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7272 (mpt180) REVERT: O 52 LYS cc_start: 0.8865 (mtmt) cc_final: 0.8452 (mttt) REVERT: O 82 ASP cc_start: 0.9216 (p0) cc_final: 0.8989 (p0) REVERT: O 101 THR cc_start: 0.9252 (m) cc_final: 0.9021 (p) REVERT: R 5 ARG cc_start: 0.9266 (OUTLIER) cc_final: 0.8455 (mtt180) REVERT: S 21 ASP cc_start: 0.8690 (t0) cc_final: 0.8343 (t0) REVERT: c 10 LYS cc_start: 0.8985 (tppp) cc_final: 0.8699 (tptp) outliers start: 15 outliers final: 9 residues processed: 257 average time/residue: 0.7079 time to fit residues: 208.1454 Evaluate side-chains 261 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 249 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 38 LYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 50 ARG Chi-restraints excluded: chain R residue 5 ARG Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 34 LYS Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain Y residue 89 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: [87, 50, 101, 67, 225, 31, 63, 197, 74, 111, 156] chunk 87 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 63 optimal weight: 0.0670 chunk 197 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 chunk 156 optimal weight: 10.0000 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 104 GLN S 72 GLN E 203 ASN g 15 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.068948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.051386 restraints weight = 58082.973| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 1.37 r_work: 0.2639 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2538 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2535 r_free = 0.2535 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2535 r_free = 0.2535 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2535 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9194 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25770 Z= 0.116 Angle : 0.529 11.263 37185 Z= 0.285 Chirality : 0.039 0.361 4634 Planarity : 0.004 0.059 2927 Dihedral : 21.969 178.825 9709 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.04 % Allowed : 13.26 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.06 % 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: 1.63 (0.20), residues: 1836 helix: 2.51 (0.20), residues: 656 sheet: 0.35 (0.26), residues: 357 loop : 0.33 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 136 TYR 0.023 0.001 TYR E 188 PHE 0.018 0.001 PHE J 67 TRP 0.012 0.001 TRP g 132 HIS 0.004 0.001 HIS T 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.12 (25762) covalent geometry : angle 0.52592 / 0.28 (37173) hydrogen bonds : bond 0.04918 / 3.29 ( 1049) hydrogen bonds : angle 3.66130 / 2.64 ( 2494) metal coordination : bond 0.00442 / 0.28 ( 8) metal coordination : angle 3.04803 / 1.69 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 252 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: B 193 ASP cc_start: 0.8942 (t0) cc_final: 0.8500 (t0) REVERT: J 38 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8201 (mptp) REVERT: L 121 LYS cc_start: 0.8437 (tttp) cc_final: 0.7823 (ttmt) REVERT: O 21 ASP cc_start: 0.8453 (p0) cc_final: 0.7935 (p0) REVERT: O 24 GLN cc_start: 0.9045 (mt0) cc_final: 0.8719 (mt0) REVERT: O 50 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7339 (mpt180) REVERT: O 52 LYS cc_start: 0.8846 (mtmt) cc_final: 0.8463 (mttt) REVERT: O 82 ASP cc_start: 0.9192 (p0) cc_final: 0.8971 (p0) REVERT: O 106 GLU cc_start: 0.8951 (tt0) cc_final: 0.8354 (tt0) REVERT: R 5 ARG cc_start: 0.9254 (OUTLIER) cc_final: 0.8433 (mtt180) REVERT: S 21 ASP cc_start: 0.8684 (t0) cc_final: 0.8329 (t0) REVERT: U 38 ASP cc_start: 0.8623 (m-30) cc_final: 0.8396 (m-30) REVERT: c 10 LYS cc_start: 0.8973 (tppp) cc_final: 0.8679 (tptp) outliers start: 14 outliers final: 8 residues processed: 258 average time/residue: 0.6848 time to fit residues: 203.1099 Evaluate side-chains 263 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 252 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 38 LYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 50 ARG Chi-restraints excluded: chain R residue 5 ARG Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain Y residue 89 GLN Chi-restraints excluded: chain c residue 52 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: [138, 38, 163, 221, 91, 47, 73, 103, 201, 199, 106] chunk 138 optimal weight: 7.9990 chunk 38 optimal weight: 0.0570 chunk 163 optimal weight: 8.9990 chunk 221 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 47 optimal weight: 0.0670 chunk 73 optimal weight: 0.3980 chunk 103 optimal weight: 2.9990 chunk 201 optimal weight: 10.0000 chunk 199 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 overall best weight: 0.9038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 104 GLN g 15 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.069619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.052162 restraints weight = 58721.189| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 1.37 r_work: 0.2660 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2559 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9180 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25770 Z= 0.115 Angle : 0.520 11.230 37185 Z= 0.278 Chirality : 0.038 0.358 4634 Planarity : 0.004 0.046 2927 Dihedral : 21.887 179.259 9709 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.67 % Allowed : 13.93 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.06 % 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: 1.72 (0.20), residues: 1836 helix: 2.61 (0.20), residues: 651 sheet: 0.38 (0.26), residues: 367 loop : 0.38 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Y 104 TYR 0.023 0.001 TYR E 188 PHE 0.025 0.001 PHE b 136 TRP 0.011 0.001 TRP g 132 HIS 0.004 0.001 HIS T 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 (25762) covalent geometry : angle 0.51720 / 0.28 (37173) hydrogen bonds : bond 0.04808 / 3.19 ( 1049) hydrogen bonds : angle 3.60994 / 2.61 ( 2494) metal coordination : bond 0.00433 / 0.29 ( 8) metal coordination : angle 3.12285 / 1.73 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14623.89 seconds wall clock time: 248 minutes 5.36 seconds (14885.36 seconds total)