Starting phenix.real_space_refine on Tue Aug 26 11:16:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e9g_27963/08_2025/8e9g_27963.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e9g_27963/08_2025/8e9g_27963.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8e9g_27963/08_2025/8e9g_27963.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e9g_27963/08_2025/8e9g_27963.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e9g_27963/08_2025/8e9g_27963.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e9g_27963/08_2025/8e9g_27963.map" } resolution = 2.6 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= 0.036 sd= 0.182 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 32 7.16 5 Zn 1 6.06 5 P 5 5.49 5 S 213 5.16 5 C 23339 2.51 5 N 6184 2.21 5 O 6167 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35941 Number of models: 1 Model: "" Number of chains: 22 Chain: "O" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 884 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 113} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1334 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 168} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 51 Chain: "A" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 930 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 114} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1659 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 21, 'TRANS': 198} Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 73 Planarities with less than four sites: {'ASP:plan': 9, 'GLU:plan': 12, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 90 Chain: "D" Number of atoms: 3037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3037 Classifications: {'peptide': 406} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 21, 'TRANS': 384} Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 92 Planarities with less than four sites: {'GLU:plan': 16, 'ASP:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "E" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1595 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 209} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 5, 'ASP:plan': 12, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 108 Chain: "G" Number of atoms: 5423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 5423 Classifications: {'peptide': 780} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PCIS': 1, 'PTRANS': 58, 'TRANS': 720} Unresolved non-hydrogen bonds: 361 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 277 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 36, 'ASP:plan': 25, 'ARG:plan': 10, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 298 Chain: "F" Number of atoms: 3110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3110 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 403} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 260 Unresolved non-hydrogen dihedrals: 166 Planarities with less than four sites: {'ASP:plan': 19, 'GLU:plan': 17, 'ARG:plan': 4, 'GLN:plan1': 4, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 172 Chain: "I" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1175 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 150} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 10, 'GLU:plan': 9, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 83 Chain: "H" Number of atoms: 2911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2911 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 367} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 6, 'PHE:plan': 2, 'ARG:plan': 5, 'GLU:plan': 5, 'GLN:plan1': 3, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 103 Chain: "J" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1607 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 9, 'TRANS': 218} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 3, 'GLU:plan': 7, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 61 Chain: "K" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 742 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 97} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "L" Number of atoms: 3853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 3853 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 208} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 602} Unresolved non-hydrogen bonds: 745 Unresolved non-hydrogen angles: 944 Unresolved non-hydrogen dihedrals: 607 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'ARG:plan': 16, 'ASP:plan': 16, 'PHE:plan': 9, 'GLU:plan': 17, 'HIS:plan': 7, 'GLN:plan1': 10, 'ASN:plan1': 3, 'TYR:plan': 5, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 387 Chain: "N" Number of atoms: 3666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3666 Classifications: {'peptide': 519} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 492} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 10, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 100 Chain: "M" Number of atoms: 3695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 3695 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 488} Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 15, 'GLU:plan': 10, 'ARG:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 130 Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 2, 66 Unusual residues: {'MQ9': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'FES': 1, 'GTP': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {' ZN': 1, 'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 58 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 1, 58 Unusual residues: {'MQ9': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 76 Unusual residues: {'XP2': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1146 SG CYS B 38 53.244 82.242 100.634 1.00 65.13 S ATOM 1140 SG CYS B 37 58.072 80.505 100.682 1.00 67.50 S ATOM 1852 SG CYS B 132 55.805 78.883 95.523 1.00 60.98 S ATOM 1642 SG CYS B 103 53.268 75.652 99.137 1.00 62.31 S ATOM 8555 SG CYS E 107 75.158 59.527 29.370 1.00 95.44 S ATOM 8591 SG CYS E 112 77.952 60.257 27.109 1.00 97.96 S ATOM 8833 SG CYS E 148 77.869 55.244 31.583 1.00 97.12 S ATOM 8857 SG CYS E 152 80.517 55.956 29.576 1.00103.60 S ATOM 9701 SG CYS G 48 68.246 48.185 60.651 1.00 60.45 S ATOM 9776 SG CYS G 59 69.631 51.655 61.631 1.00 62.12 S ATOM 9802 SG CYS G 62 73.321 47.356 63.815 1.00 63.66 S ATOM 9893 SG CYS G 76 70.815 45.222 62.172 1.00 62.68 S ATOM 10167 SG CYS G 114 62.198 66.835 67.688 1.00 57.34 S ATOM 10224 SG CYS G 123 61.514 60.138 67.739 1.00 56.32 S ATOM 10188 SG CYS G 117 56.832 63.094 66.091 1.00 56.88 S ATOM 10909 SG CYS G 213 57.725 55.326 62.473 1.00 56.55 S ATOM 10561 SG CYS G 166 62.181 51.879 60.896 1.00 58.98 S ATOM 10540 SG CYS G 163 60.191 56.297 56.540 1.00 59.76 S ATOM 10583 SG CYS G 169 56.804 51.010 57.531 1.00 57.81 S ATOM 11103 SG CYS G 239 41.701 43.166 73.379 1.00 63.70 S ATOM 11149 SG CYS G 246 46.668 39.932 72.205 1.00 61.89 S ATOM 11363 SG CYS G 274 42.646 42.624 67.320 1.00 62.98 S ATOM 11128 SG CYS G 242 40.199 38.935 69.556 1.00 69.74 S ATOM 17240 SG CYS F 334 85.639 72.648 38.648 1.00 91.04 S ATOM 17906 SG CYS F 426 83.753 75.440 37.276 1.00 88.01 S ATOM 17403 SG CYS F 354 73.155 52.348 52.792 1.00 66.18 S ATOM 17719 SG CYS F 397 75.366 49.007 47.563 1.00 74.15 S ATOM 17423 SG CYS F 357 73.795 55.314 48.503 1.00 68.65 S ATOM 17384 SG CYS F 351 69.205 50.427 48.079 1.00 72.78 S ATOM 18679 SG CYS I 99 52.622 80.076 87.945 1.00 55.94 S ATOM 18697 SG CYS I 102 58.541 77.020 87.396 1.00 58.06 S ATOM 18715 SG CYS I 105 55.900 79.018 82.409 1.00 55.62 S ATOM 18411 SG CYS I 64 53.938 74.044 86.146 1.00 55.41 S ATOM 18358 SG CYS I 57 55.471 72.915 72.785 1.00 54.71 S ATOM 18739 SG CYS I 109 56.174 78.101 75.726 1.00 58.29 S ATOM 18381 SG CYS I 60 52.985 75.021 77.995 1.00 53.34 S ATOM 18340 SG CYS I 54 50.079 76.894 72.761 1.00 56.45 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" C1 AMQ9 B 202 " occ=0.50 ... (56 atoms not shown) pdb=" O4 AMQ9 B 202 " occ=0.50 residue: pdb=" C1 BMQ9 H 501 " occ=0.50 ... (56 atoms not shown) pdb=" O4 BMQ9 H 501 " occ=0.50 Time building chain proxies: 7.85, per 1000 atoms: 0.22 Number of scatterers: 35941 At special positions: 0 Unit cell: (112.12, 147.526, 279.709, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 32 26.01 S 213 16.00 P 5 15.00 O 6167 8.00 N 6184 7.00 C 23339 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.09 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E1000 " pdb="FE2 FES E1000 " - pdb=" SG CYS E 152 " pdb="FE1 FES E1000 " - pdb=" SG CYS E 107 " pdb="FE1 FES E1000 " - pdb=" SG CYS E 112 " pdb="FE2 FES E1000 " - pdb=" SG CYS E 148 " pdb=" FES G 801 " pdb="FE1 FES G 801 " - pdb=" SG CYS G 48 " pdb="FE1 FES G 801 " - pdb=" SG CYS G 59 " pdb="FE2 FES G 801 " - pdb=" SG CYS G 62 " pdb="FE2 FES G 801 " - pdb=" SG CYS G 76 " pdb=" SF4 B 201 " pdb="FE2 SF4 B 201 " - pdb=" SG CYS B 37 " pdb="FE3 SF4 B 201 " - pdb=" SG CYS B 132 " pdb="FE4 SF4 B 201 " - pdb=" SG CYS B 103 " pdb="FE1 SF4 B 201 " - pdb=" SG CYS B 38 " pdb=" SF4 F 502 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 351 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 397 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 354 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 357 " pdb=" SF4 G 803 " pdb="FE3 SF4 G 803 " - pdb=" NE2 HIS G 110 " pdb="FE2 SF4 G 803 " - pdb=" SG CYS G 123 " pdb="FE1 SF4 G 803 " - pdb=" SG CYS G 114 " pdb="FE4 SF4 G 803 " - pdb=" SG CYS G 117 " pdb=" SF4 G 804 " pdb="FE3 SF4 G 804 " - pdb=" SG CYS G 163 " pdb="FE2 SF4 G 804 " - pdb=" SG CYS G 166 " pdb="FE4 SF4 G 804 " - pdb=" SG CYS G 169 " pdb="FE1 SF4 G 804 " - pdb=" SG CYS G 213 " pdb=" SF4 G 805 " pdb="FE2 SF4 G 805 " - pdb=" SG CYS G 246 " pdb="FE1 SF4 G 805 " - pdb=" SG CYS G 239 " pdb="FE3 SF4 G 805 " - pdb=" SG CYS G 274 " pdb="FE4 SF4 G 805 " - pdb=" SG CYS G 242 " pdb=" SF4 I 201 " pdb="FE3 SF4 I 201 " - pdb=" NE2 HIS I 42 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 99 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 105 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 102 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 64 " pdb=" SF4 I 202 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 57 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 109 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 54 " Number of angles added : 93 Zn2+ tetrahedral coordination pdb=" ZN F 501 " pdb="ZN ZN F 501 " - pdb=" SG CYS F 426 " pdb="ZN ZN F 501 " - pdb=" NE2 HIS F 421 " pdb="ZN ZN F 501 " - pdb=" SG CYS F 334 " 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9140 Finding SS restraints... Secondary structure from input PDB file: 232 helices and 28 sheets defined 62.7% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'O' and resid 15 through 26 Processing helix chain 'O' and resid 44 through 55 Processing helix chain 'O' and resid 70 through 82 Processing helix chain 'O' and resid 94 through 96 No H-bonds generated for 'chain 'O' and resid 94 through 96' Processing helix chain 'O' and resid 97 through 104 Processing helix chain 'O' and resid 115 through 128 Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 10 through 26 Processing helix chain 'B' and resid 36 through 47 removed outlier: 3.557A pdb=" N ILE B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 56 Processing helix chain 'B' and resid 77 through 79 No H-bonds generated for 'chain 'B' and resid 77 through 79' Processing helix chain 'B' and resid 80 through 91 Processing helix chain 'B' and resid 101 through 107 Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 135 through 152 Processing helix chain 'B' and resid 155 through 173 removed outlier: 3.893A pdb=" N ALA B 172 " --> pdb=" O GLN B 168 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 179 Processing helix chain 'A' and resid 4 through 28 Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 64 through 79 removed outlier: 3.596A pdb=" N VAL A 73 " --> pdb=" O MET A 69 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 87 Processing helix chain 'A' and resid 87 through 92 removed outlier: 3.602A pdb=" N GLY A 92 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 116 Processing helix chain 'C' and resid 31 through 34 removed outlier: 3.825A pdb=" N ASN C 34 " --> pdb=" O MET C 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 31 through 34' Processing helix chain 'C' and resid 63 through 75 Processing helix chain 'C' and resid 76 through 83 Processing helix chain 'C' and resid 102 through 113 Processing helix chain 'C' and resid 172 through 176 Processing helix chain 'C' and resid 177 through 187 Processing helix chain 'D' and resid 80 through 86 removed outlier: 4.041A pdb=" N GLU D 86 " --> pdb=" O GLU D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 98 removed outlier: 3.790A pdb=" N PHE D 96 " --> pdb=" O GLN D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 121 Processing helix chain 'D' and resid 122 through 126 removed outlier: 3.739A pdb=" N ILE D 126 " --> pdb=" O THR D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 157 Processing helix chain 'D' and resid 159 through 182 removed outlier: 3.789A pdb=" N MET D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE D 164 " --> pdb=" O MET D 160 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D 172 " --> pdb=" O ARG D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 226 Proline residue: D 215 - end of helix removed outlier: 3.636A pdb=" N ASP D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU D 221 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 236 Processing helix chain 'D' and resid 242 through 250 Processing helix chain 'D' and resid 253 through 258 Processing helix chain 'D' and resid 273 through 277 Processing helix chain 'D' and resid 288 through 314 removed outlier: 3.592A pdb=" N HIS D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 352 removed outlier: 3.590A pdb=" N ARG D 352 " --> pdb=" O LYS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 366 Processing helix chain 'D' and resid 405 through 411 removed outlier: 3.580A pdb=" N THR D 409 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 419 Processing helix chain 'D' and resid 422 through 434 Processing helix chain 'D' and resid 436 through 442 Processing helix chain 'E' and resid 26 through 43 removed outlier: 3.761A pdb=" N GLN E 39 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG E 43 " --> pdb=" O GLN E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 49 Processing helix chain 'E' and resid 50 through 62 Processing helix chain 'E' and resid 66 through 78 Processing helix chain 'E' and resid 83 through 89 removed outlier: 3.569A pdb=" N VAL E 87 " --> pdb=" O GLU E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 115 Processing helix chain 'E' and resid 116 through 129 Processing helix chain 'E' and resid 151 through 155 Processing helix chain 'E' and resid 169 through 182 Processing helix chain 'E' and resid 195 through 204 Processing helix chain 'E' and resid 216 through 230 removed outlier: 4.254A pdb=" N THR E 220 " --> pdb=" O PRO E 216 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLY E 223 " --> pdb=" O ALA E 219 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LEU E 224 " --> pdb=" O THR E 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 41 Processing helix chain 'G' and resid 92 through 109 removed outlier: 4.724A pdb=" N ASN G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 133 Processing helix chain 'G' and resid 167 through 175 Processing helix chain 'G' and resid 187 through 191 Processing helix chain 'G' and resid 205 through 213 removed outlier: 4.014A pdb=" N THR G 209 " --> pdb=" O PHE G 205 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL G 210 " --> pdb=" O SER G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 232 Processing helix chain 'G' and resid 274 through 280 Processing helix chain 'G' and resid 282 through 286 removed outlier: 3.676A pdb=" N VAL G 286 " --> pdb=" O TYR G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 320 Processing helix chain 'G' and resid 333 through 347 Processing helix chain 'G' and resid 361 through 372 Processing helix chain 'G' and resid 380 through 387 removed outlier: 3.680A pdb=" N ASN G 386 " --> pdb=" O ALA G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 401 through 416 Processing helix chain 'G' and resid 427 through 433 Processing helix chain 'G' and resid 444 through 451 Processing helix chain 'G' and resid 455 through 460 removed outlier: 3.524A pdb=" N ARG G 459 " --> pdb=" O ASP G 455 " (cutoff:3.500A) Processing helix chain 'G' and resid 470 through 474 Processing helix chain 'G' and resid 476 through 489 Processing helix chain 'G' and resid 499 through 507 removed outlier: 4.422A pdb=" N GLY G 503 " --> pdb=" O ALA G 499 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 534 Processing helix chain 'G' and resid 545 through 555 Processing helix chain 'G' and resid 567 through 571 Processing helix chain 'G' and resid 573 through 584 Processing helix chain 'G' and resid 595 through 600 Processing helix chain 'G' and resid 609 through 613 Processing helix chain 'G' and resid 637 through 650 Processing helix chain 'G' and resid 657 through 669 Processing helix chain 'G' and resid 706 through 710 Processing helix chain 'G' and resid 712 through 718 Processing helix chain 'G' and resid 727 through 734 Processing helix chain 'G' and resid 775 through 781 Processing helix chain 'F' and resid 7 through 12 removed outlier: 4.205A pdb=" N PHE F 11 " --> pdb=" O LEU F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 25 Processing helix chain 'F' and resid 29 through 38 Processing helix chain 'F' and resid 39 through 51 Processing helix chain 'F' and resid 61 through 68 Processing helix chain 'F' and resid 101 through 109 removed outlier: 3.508A pdb=" N LEU F 105 " --> pdb=" O LYS F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 125 removed outlier: 4.182A pdb=" N LEU F 113 " --> pdb=" O THR F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 154 Processing helix chain 'F' and resid 160 through 164 Processing helix chain 'F' and resid 179 through 183 Processing helix chain 'F' and resid 186 through 192 Processing helix chain 'F' and resid 204 through 209 Processing helix chain 'F' and resid 210 through 213 Processing helix chain 'F' and resid 220 through 231 Proline residue: F 227 - end of helix Processing helix chain 'F' and resid 232 through 239 removed outlier: 3.868A pdb=" N TRP F 236 " --> pdb=" O ASN F 232 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE F 237 " --> pdb=" O GLY F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 279 Processing helix chain 'F' and resid 303 through 305 No H-bonds generated for 'chain 'F' and resid 303 through 305' Processing helix chain 'F' and resid 310 through 318 Processing helix chain 'F' and resid 334 through 350 Processing helix chain 'F' and resid 354 through 373 removed outlier: 3.654A pdb=" N TYR F 362 " --> pdb=" O ARG F 358 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 392 removed outlier: 3.858A pdb=" N ILE F 381 " --> pdb=" O THR F 377 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP F 382 " --> pdb=" O GLU F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 422 removed outlier: 4.349A pdb=" N ASP F 401 " --> pdb=" O CYS F 397 " (cutoff:3.500A) Proline residue: F 406 - end of helix removed outlier: 6.894A pdb=" N ASP F 416 " --> pdb=" O LYS F 412 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLU F 417 " --> pdb=" O HIS F 413 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU F 422 " --> pdb=" O TYR F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 434 Processing helix chain 'I' and resid 4 through 7 removed outlier: 3.558A pdb=" N ALA I 7 " --> pdb=" O PHE I 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 4 through 7' Processing helix chain 'I' and resid 8 through 20 removed outlier: 3.616A pdb=" N ALA I 12 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE I 19 " --> pdb=" O LEU I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 64 Processing helix chain 'I' and resid 103 through 109 Processing helix chain 'I' and resid 127 through 129 No H-bonds generated for 'chain 'I' and resid 127 through 129' Processing helix chain 'I' and resid 133 through 138 Processing helix chain 'I' and resid 157 through 164 Processing helix chain 'H' and resid 13 through 47 Processing helix chain 'H' and resid 56 through 60 Processing helix chain 'H' and resid 61 through 72 Processing helix chain 'H' and resid 82 through 101 Proline residue: H 90 - end of helix Proline residue: H 96 - end of helix removed outlier: 3.950A pdb=" N PHE H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 104 No H-bonds generated for 'chain 'H' and resid 102 through 104' Processing helix chain 'H' and resid 126 through 149 removed outlier: 3.975A pdb=" N TYR H 140 " --> pdb=" O SER H 136 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY H 141 " --> pdb=" O ILE H 137 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE H 142 " --> pdb=" O GLY H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 151 through 184 removed outlier: 4.933A pdb=" N ILE H 170 " --> pdb=" O VAL H 166 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ALA H 171 " --> pdb=" O SER H 167 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE H 176 " --> pdb=" O MET H 172 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL H 177 " --> pdb=" O GLY H 173 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA H 178 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL H 179 " --> pdb=" O SER H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 195 Processing helix chain 'H' and resid 199 through 204 removed outlier: 3.717A pdb=" N LEU H 203 " --> pdb=" O TRP H 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 219 Processing helix chain 'H' and resid 229 through 234 Processing helix chain 'H' and resid 235 through 239 removed outlier: 3.519A pdb=" N HIS H 238 " --> pdb=" O GLY H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 242 through 269 removed outlier: 3.665A pdb=" N PHE H 246 " --> pdb=" O SER H 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 275 through 280 removed outlier: 3.803A pdb=" N LEU H 280 " --> pdb=" O PHE H 276 " (cutoff:3.500A) Processing helix chain 'H' and resid 288 through 312 removed outlier: 3.668A pdb=" N LEU H 292 " --> pdb=" O TRP H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 316 through 327 Processing helix chain 'H' and resid 327 through 348 Processing helix chain 'H' and resid 351 through 375 removed outlier: 3.723A pdb=" N THR H 359 " --> pdb=" O ALA H 355 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 40 Processing helix chain 'J' and resid 42 through 64 Processing helix chain 'J' and resid 66 through 92 Processing helix chain 'J' and resid 106 through 127 Processing helix chain 'J' and resid 129 through 133 Processing helix chain 'J' and resid 137 through 142 Processing helix chain 'J' and resid 144 through 156 Processing helix chain 'J' and resid 157 through 179 removed outlier: 3.791A pdb=" N SER J 165 " --> pdb=" O PHE J 161 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA J 166 " --> pdb=" O GLU J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 186 Processing helix chain 'J' and resid 189 through 195 Processing helix chain 'J' and resid 198 through 203 Processing helix chain 'J' and resid 231 through 235 removed outlier: 3.550A pdb=" N VAL J 235 " --> pdb=" O PRO J 232 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 24 Processing helix chain 'K' and resid 26 through 53 Processing helix chain 'K' and resid 55 through 87 removed outlier: 3.708A pdb=" N THR K 85 " --> pdb=" O ALA K 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 25 Proline residue: L 15 - end of helix Processing helix chain 'L' and resid 26 through 30 Processing helix chain 'L' and resid 32 through 57 Processing helix chain 'L' and resid 59 through 64 removed outlier: 3.514A pdb=" N ALA L 64 " --> pdb=" O GLU L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 112 removed outlier: 3.666A pdb=" N CYS L 92 " --> pdb=" O GLN L 88 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE L 93 " --> pdb=" O LEU L 89 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY L 110 " --> pdb=" O ILE L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 117 through 138 Processing helix chain 'L' and resid 140 through 160 Processing helix chain 'L' and resid 165 through 198 Processing helix chain 'L' and resid 201 through 209 Processing helix chain 'L' and resid 213 through 233 Processing helix chain 'L' and resid 239 through 245 removed outlier: 4.526A pdb=" N ASP L 243 " --> pdb=" O SER L 239 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET L 245 " --> pdb=" O LEU L 241 " (cutoff:3.500A) Processing helix chain 'L' and resid 248 through 258 Processing helix chain 'L' and resid 261 through 271 removed outlier: 4.117A pdb=" N VAL L 265 " --> pdb=" O VAL L 261 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 277 Processing helix chain 'L' and resid 278 through 303 removed outlier: 3.882A pdb=" N ALA L 302 " --> pdb=" O ILE L 298 " (cutoff:3.500A) Processing helix chain 'L' and resid 305 through 327 Processing helix chain 'L' and resid 328 through 360 removed outlier: 4.322A pdb=" N ALA L 333 " --> pdb=" O PRO L 329 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N PHE L 334 " --> pdb=" O ALA L 330 " (cutoff:3.500A) Processing helix chain 'L' and resid 371 through 376 removed outlier: 4.214A pdb=" N VAL L 375 " --> pdb=" O GLY L 371 " (cutoff:3.500A) Processing helix chain 'L' and resid 376 through 392 Processing helix chain 'L' and resid 396 through 412 removed outlier: 4.281A pdb=" N PHE L 400 " --> pdb=" O LEU L 396 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER L 401 " --> pdb=" O ALA L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 413 through 444 Processing helix chain 'L' and resid 459 through 482 Proline residue: L 465 - end of helix removed outlier: 5.382A pdb=" N GLY L 477 " --> pdb=" O SER L 473 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY L 478 " --> pdb=" O VAL L 474 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 491 Processing helix chain 'L' and resid 504 through 528 Processing helix chain 'L' and resid 540 through 548 Processing helix chain 'L' and resid 551 through 578 removed outlier: 3.960A pdb=" N MET L 561 " --> pdb=" O GLU L 557 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARG L 562 " --> pdb=" O ALA L 558 " (cutoff:3.500A) Processing helix chain 'L' and resid 578 through 601 removed outlier: 3.865A pdb=" N ALA L 583 " --> pdb=" O VAL L 579 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN L 601 " --> pdb=" O LEU L 597 " (cutoff:3.500A) Processing helix chain 'L' and resid 604 through 614 Processing helix chain 'L' and resid 615 through 628 removed outlier: 4.056A pdb=" N VAL L 626 " --> pdb=" O ALA L 622 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN L 627 " --> pdb=" O ILE L 623 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 31 Proline residue: N 13 - end of helix removed outlier: 6.309A pdb=" N VAL N 17 " --> pdb=" O PRO N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 32 through 62 removed outlier: 4.484A pdb=" N TYR N 37 " --> pdb=" O ARG N 33 " (cutoff:3.500A) Proline residue: N 38 - end of helix Processing helix chain 'N' and resid 78 through 100 Processing helix chain 'N' and resid 128 through 138 Processing helix chain 'N' and resid 143 through 161 Proline residue: N 159 - end of helix Processing helix chain 'N' and resid 163 through 182 Proline residue: N 177 - end of helix Processing helix chain 'N' and resid 188 through 222 Processing helix chain 'N' and resid 225 through 235 Processing helix chain 'N' and resid 241 through 259 Processing helix chain 'N' and resid 260 through 264 Processing helix chain 'N' and resid 265 through 274 removed outlier: 4.168A pdb=" N ASP N 269 " --> pdb=" O SER N 265 " (cutoff:3.500A) Processing helix chain 'N' and resid 275 through 300 removed outlier: 3.633A pdb=" N ALA N 284 " --> pdb=" O ALA N 280 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) Processing helix chain 'N' and resid 302 through 304 No H-bonds generated for 'chain 'N' and resid 302 through 304' Processing helix chain 'N' and resid 305 through 330 Proline residue: N 311 - end of helix removed outlier: 3.558A pdb=" N ALA N 315 " --> pdb=" O PRO N 311 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR N 325 " --> pdb=" O MET N 321 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA N 328 " --> pdb=" O GLY N 324 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR N 330 " --> pdb=" O VAL N 326 " (cutoff:3.500A) Processing helix chain 'N' and resid 333 through 355 removed outlier: 3.512A pdb=" N ALA N 355 " --> pdb=" O THR N 351 " (cutoff:3.500A) Processing helix chain 'N' and resid 357 through 383 Processing helix chain 'N' and resid 395 through 400 Processing helix chain 'N' and resid 401 through 406 Processing helix chain 'N' and resid 406 through 422 Processing helix chain 'N' and resid 426 through 442 Processing helix chain 'N' and resid 444 through 471 removed outlier: 3.932A pdb=" N TYR N 460 " --> pdb=" O ALA N 456 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE N 461 " --> pdb=" O VAL N 457 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL N 465 " --> pdb=" O PHE N 461 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE N 466 " --> pdb=" O TYR N 462 " (cutoff:3.500A) Processing helix chain 'N' and resid 485 through 505 Processing helix chain 'N' and resid 506 through 516 removed outlier: 6.315A pdb=" N LEU N 512 " --> pdb=" O PRO N 508 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 25 Proline residue: M 15 - end of helix Processing helix chain 'M' and resid 26 through 28 No H-bonds generated for 'chain 'M' and resid 26 through 28' Processing helix chain 'M' and resid 29 through 55 Processing helix chain 'M' and resid 72 through 75 Processing helix chain 'M' and resid 83 through 104 Proline residue: M 98 - end of helix Processing helix chain 'M' and resid 113 through 116 Processing helix chain 'M' and resid 117 through 139 Processing helix chain 'M' and resid 141 through 152 Processing helix chain 'M' and resid 152 through 162 Processing helix chain 'M' and resid 167 through 199 Processing helix chain 'M' and resid 209 through 220 Processing helix chain 'M' and resid 225 through 244 Processing helix chain 'M' and resid 248 through 250 No H-bonds generated for 'chain 'M' and resid 248 through 250' Processing helix chain 'M' and resid 251 through 260 removed outlier: 4.685A pdb=" N ASP M 255 " --> pdb=" O ARG M 251 " (cutoff:3.500A) Processing helix chain 'M' and resid 261 through 271 Processing helix chain 'M' and resid 273 through 283 removed outlier: 3.734A pdb=" N THR M 277 " --> pdb=" O ASP M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 283 through 288 Processing helix chain 'M' and resid 288 through 317 Proline residue: M 297 - end of helix Processing helix chain 'M' and resid 319 through 341 Processing helix chain 'M' and resid 343 through 375 Processing helix chain 'M' and resid 379 through 383 Processing helix chain 'M' and resid 385 through 390 removed outlier: 3.982A pdb=" N VAL M 389 " --> pdb=" O GLY M 385 " (cutoff:3.500A) Processing helix chain 'M' and resid 390 through 405 Processing helix chain 'M' and resid 410 through 427 removed outlier: 4.292A pdb=" N ILE M 414 " --> pdb=" O LEU M 410 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER M 415 " --> pdb=" O ALA M 411 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG M 426 " --> pdb=" O GLY M 422 " (cutoff:3.500A) Processing helix chain 'M' and resid 427 through 454 removed outlier: 4.103A pdb=" N ALA M 437 " --> pdb=" O PHE M 433 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU M 438 " --> pdb=" O ALA M 434 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL M 439 " --> pdb=" O ALA M 435 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR M 448 " --> pdb=" O TYR M 444 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR M 454 " --> pdb=" O GLN M 450 " (cutoff:3.500A) Processing helix chain 'M' and resid 472 through 492 Proline residue: M 481 - end of helix Processing helix chain 'M' and resid 493 through 512 removed outlier: 3.704A pdb=" N VAL M 499 " --> pdb=" O PRO M 495 " (cutoff:3.500A) Proline residue: M 502 - end of helix Processing sheet with id=AA1, first strand: chain 'O' and resid 37 through 42 removed outlier: 6.200A pdb=" N LEU O 7 " --> pdb=" O GLU O 38 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N VAL O 40 " --> pdb=" O LEU O 7 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE O 9 " --> pdb=" O VAL O 40 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL O 42 " --> pdb=" O ILE O 9 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL O 11 " --> pdb=" O VAL O 42 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG O 8 " --> pdb=" O LEU O 59 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILE O 61 " --> pdb=" O ARG O 8 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU O 10 " --> pdb=" O ILE O 61 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ASP O 63 " --> pdb=" O LEU O 10 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N TYR O 12 " --> pdb=" O ASP O 63 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA O 60 " --> pdb=" O LEU O 89 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU O 91 " --> pdb=" O ALA O 60 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU O 62 " --> pdb=" O LEU O 91 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE O 88 " --> pdb=" O ALA O 108 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N VAL O 110 " --> pdb=" O ILE O 88 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL O 90 " --> pdb=" O VAL O 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 69 through 71 removed outlier: 3.559A pdb=" N ILE B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 23 through 29 removed outlier: 5.984A pdb=" N ILE C 24 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU C 52 " --> pdb=" O ILE C 24 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA C 26 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 90 removed outlier: 6.573A pdb=" N LEU C 94 " --> pdb=" O GLN C 153 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLU C 155 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE C 96 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ALA C 157 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL C 98 " --> pdb=" O ALA C 157 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 84 through 90 removed outlier: 6.573A pdb=" N LEU C 94 " --> pdb=" O GLN C 153 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLU C 155 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE C 96 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ALA C 157 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL C 98 " --> pdb=" O ALA C 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 221 through 223 Processing sheet with id=AA7, first strand: chain 'D' and resid 41 through 44 removed outlier: 6.762A pdb=" N ARG D 57 " --> pdb=" O CYS D 72 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N CYS D 72 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE D 59 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA D 70 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLU D 61 " --> pdb=" O THR D 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 190 through 191 Processing sheet with id=AA9, first strand: chain 'D' and resid 332 through 335 Processing sheet with id=AB1, first strand: chain 'D' and resid 373 through 381 Processing sheet with id=AB2, first strand: chain 'E' and resid 141 through 146 removed outlier: 6.812A pdb=" N TYR E 102 " --> pdb=" O THR E 142 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N GLU E 144 " --> pdb=" O TYR E 102 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL E 104 " --> pdb=" O GLU E 144 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL E 146 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL E 106 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 23 through 28 removed outlier: 9.188A pdb=" N VAL G 86 " --> pdb=" O SER G 17 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N THR G 19 " --> pdb=" O VAL G 86 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 150 through 151 Processing sheet with id=AB5, first strand: chain 'G' and resid 183 through 185 Processing sheet with id=AB6, first strand: chain 'G' and resid 233 through 238 removed outlier: 5.614A pdb=" N ARG G 249 " --> pdb=" O ARG G 260 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG G 260 " --> pdb=" O ARG G 249 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ASP G 251 " --> pdb=" O LEU G 258 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 300 through 303 removed outlier: 6.399A pdb=" N VAL G 587 " --> pdb=" O VAL G 603 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N PHE G 605 " --> pdb=" O VAL G 587 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER G 589 " --> pdb=" O PHE G 605 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU G 561 " --> pdb=" O VAL G 588 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N LEU G 590 " --> pdb=" O LEU G 561 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL G 563 " --> pdb=" O LEU G 590 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY G 325 " --> pdb=" O LEU G 562 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N GLY G 564 " --> pdb=" O GLY G 325 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU G 327 " --> pdb=" O GLY G 564 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N ASP G 354 " --> pdb=" O THR G 324 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL G 326 " --> pdb=" O ASP G 354 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 436 through 437 removed outlier: 6.843A pdb=" N VAL G 419 " --> pdb=" O THR G 436 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR G 389 " --> pdb=" O VAL G 464 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU G 466 " --> pdb=" O THR G 389 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU G 391 " --> pdb=" O LEU G 466 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N GLY G 468 " --> pdb=" O LEU G 391 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ALA G 393 " --> pdb=" O GLY G 468 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 513 through 514 Processing sheet with id=AC1, first strand: chain 'G' and resid 615 through 618 Processing sheet with id=AC2, first strand: chain 'G' and resid 693 through 699 removed outlier: 3.896A pdb=" N TRP G 699 " --> pdb=" O LEU G 767 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 169 through 175 removed outlier: 7.149A pdb=" N ARG F 127 " --> pdb=" O ASP F 169 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ILE F 171 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA F 129 " --> pdb=" O ILE F 171 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N HIS F 173 " --> pdb=" O ALA F 129 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ILE F 131 " --> pdb=" O HIS F 173 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLY F 175 " --> pdb=" O ILE F 131 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL F 133 " --> pdb=" O GLY F 175 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N HIS F 86 " --> pdb=" O ALA F 126 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N HIS F 128 " --> pdb=" O HIS F 86 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG F 134 " --> pdb=" O ALA F 92 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 261 through 266 removed outlier: 6.601A pdb=" N ILE F 328 " --> pdb=" O SER F 252 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N SER F 254 " --> pdb=" O ILE F 328 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ASP F 330 " --> pdb=" O SER F 254 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 42 through 44 Processing sheet with id=AC6, first strand: chain 'I' and resid 69 through 75 removed outlier: 6.613A pdb=" N ALA I 74 " --> pdb=" O GLY I 89 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLY I 89 " --> pdb=" O ALA I 74 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 109 through 112 Processing sheet with id=AC8, first strand: chain 'L' and resid 65 through 73 removed outlier: 7.900A pdb=" N GLU L 67 " --> pdb=" O LEU L 86 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU L 86 " --> pdb=" O GLU L 67 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU L 69 " --> pdb=" O LEU L 84 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N LEU L 84 " --> pdb=" O LEU L 69 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N SER L 71 " --> pdb=" O PHE L 82 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N PHE L 82 " --> pdb=" O SER L 71 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 385 through 386 Processing sheet with id=AD1, first strand: chain 'M' and resid 63 through 71 removed outlier: 5.600A pdb=" N PHE M 64 " --> pdb=" O VAL M 82 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL M 82 " --> pdb=" O PHE M 64 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TRP M 70 " --> pdb=" O THR M 76 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR M 76 " --> pdb=" O TRP M 70 " (cutoff:3.500A) 2305 hydrogen bonds defined for protein. 6624 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.24 Time building geometry restraints manager: 4.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.39: 14476 1.39 - 1.62: 21958 1.62 - 1.84: 304 1.84 - 2.06: 0 2.06 - 2.29: 92 Bond restraints: 36830 Sorted by residual: bond pdb=" C50 XP2 L 701 " pdb=" O49 XP2 L 701 " ideal model delta sigma weight residual 1.344 1.439 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C39 XP2 L 701 " pdb=" O38 XP2 L 701 " ideal model delta sigma weight residual 1.348 1.438 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C4 FMN F 503 " pdb=" C4A FMN F 503 " ideal model delta sigma weight residual 1.485 1.397 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C28 XP2 L 701 " pdb=" C30 XP2 L 701 " ideal model delta sigma weight residual 1.561 1.477 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C58 XP2 L 701 " pdb=" C59 XP2 L 701 " ideal model delta sigma weight residual 1.526 1.603 -0.077 2.00e-02 2.50e+03 1.49e+01 ... (remaining 36825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 49831 2.20 - 4.41: 669 4.41 - 6.61: 46 6.61 - 8.82: 7 8.82 - 11.02: 6 Bond angle restraints: 50559 Sorted by residual: angle pdb=" N PRO E 235 " pdb=" CA PRO E 235 " pdb=" CB PRO E 235 " ideal model delta sigma weight residual 103.25 94.97 8.28 1.05e+00 9.07e-01 6.21e+01 angle pdb=" C PRO E 235 " pdb=" CA PRO E 235 " pdb=" CB PRO E 235 " ideal model delta sigma weight residual 111.56 103.03 8.53 1.65e+00 3.67e-01 2.67e+01 angle pdb=" O62 XP2 L 701 " pdb=" P34 XP2 L 701 " pdb=" O63 XP2 L 701 " ideal model delta sigma weight residual 121.17 110.15 11.02 3.00e+00 1.11e-01 1.35e+01 angle pdb=" C07 XP2 L 701 " pdb=" O08 XP2 L 701 " pdb=" C09 XP2 L 701 " ideal model delta sigma weight residual 115.87 104.91 10.96 3.00e+00 1.11e-01 1.33e+01 angle pdb=" C48 XP2 L 701 " pdb=" O49 XP2 L 701 " pdb=" C50 XP2 L 701 " ideal model delta sigma weight residual 123.60 113.03 10.57 3.00e+00 1.11e-01 1.24e+01 ... (remaining 50554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.62: 21133 31.62 - 63.24: 267 63.24 - 94.86: 26 94.86 - 126.48: 0 126.48 - 158.10: 1 Dihedral angle restraints: 21427 sinusoidal: 7106 harmonic: 14321 Sorted by residual: dihedral pdb=" C8 GTP G 802 " pdb=" C1' GTP G 802 " pdb=" N9 GTP G 802 " pdb=" O4' GTP G 802 " ideal model delta sinusoidal sigma weight residual 104.59 -97.31 -158.10 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" CA HIS J 203 " pdb=" C HIS J 203 " pdb=" N PRO J 204 " pdb=" CA PRO J 204 " ideal model delta harmonic sigma weight residual -180.00 -151.64 -28.36 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" C PRO E 235 " pdb=" N PRO E 235 " pdb=" CA PRO E 235 " pdb=" CB PRO E 235 " ideal model delta harmonic sigma weight residual -120.70 -106.65 -14.05 0 2.50e+00 1.60e-01 3.16e+01 ... (remaining 21424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 5014 0.050 - 0.101: 930 0.101 - 0.151: 146 0.151 - 0.202: 3 0.202 - 0.252: 2 Chirality restraints: 6095 Sorted by residual: chirality pdb=" C73 XP2 L 701 " pdb=" C71 XP2 L 701 " pdb=" C74 XP2 L 701 " pdb=" O76 XP2 L 701 " both_signs ideal model delta sigma weight residual False -2.33 -2.58 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C11 XP2 L 701 " pdb=" C12 XP2 L 701 " pdb=" C26 XP2 L 701 " pdb=" O10 XP2 L 701 " both_signs ideal model delta sigma weight residual False 2.38 2.59 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" C66 XP2 L 701 " pdb=" C67 XP2 L 701 " pdb=" O65 XP2 L 701 " pdb=" O76 XP2 L 701 " both_signs ideal model delta sigma weight residual False -2.16 -2.36 0.20 2.00e-01 2.50e+01 9.57e-01 ... (remaining 6092 not shown) Planarity restraints: 6395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 AMQ9 B 202 " -0.078 2.00e-02 2.50e+03 1.99e-01 1.39e+03 pdb=" C2 AMQ9 B 202 " -0.037 2.00e-02 2.50e+03 pdb=" C3 AMQ9 B 202 " 0.032 2.00e-02 2.50e+03 pdb=" C3AAMQ9 B 202 " 0.077 2.00e-02 2.50e+03 pdb=" C3BAMQ9 B 202 " 0.051 2.00e-02 2.50e+03 pdb=" C3CAMQ9 B 202 " -0.015 2.00e-02 2.50e+03 pdb=" C3DAMQ9 B 202 " -0.055 2.00e-02 2.50e+03 pdb=" C4 AMQ9 B 202 " 0.047 2.00e-02 2.50e+03 pdb=" C5 AMQ9 B 202 " -0.082 2.00e-02 2.50e+03 pdb=" C5MAMQ9 B 202 " -0.436 2.00e-02 2.50e+03 pdb=" C6 AMQ9 B 202 " 0.105 2.00e-02 2.50e+03 pdb=" C7 AMQ9 B 202 " 0.495 2.00e-02 2.50e+03 pdb=" O1 AMQ9 B 202 " -0.244 2.00e-02 2.50e+03 pdb=" O4 AMQ9 B 202 " 0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BMQ9 H 501 " -0.034 2.00e-02 2.50e+03 1.91e-01 1.28e+03 pdb=" C2 BMQ9 H 501 " 0.004 2.00e-02 2.50e+03 pdb=" C3 BMQ9 H 501 " -0.049 2.00e-02 2.50e+03 pdb=" C3ABMQ9 H 501 " -0.012 2.00e-02 2.50e+03 pdb=" C3BBMQ9 H 501 " 0.072 2.00e-02 2.50e+03 pdb=" C3CBMQ9 H 501 " 0.120 2.00e-02 2.50e+03 pdb=" C3DBMQ9 H 501 " 0.086 2.00e-02 2.50e+03 pdb=" C4 BMQ9 H 501 " -0.133 2.00e-02 2.50e+03 pdb=" C5 BMQ9 H 501 " 0.104 2.00e-02 2.50e+03 pdb=" C5MBMQ9 H 501 " 0.518 2.00e-02 2.50e+03 pdb=" C6 BMQ9 H 501 " -0.041 2.00e-02 2.50e+03 pdb=" C7 BMQ9 H 501 " -0.198 2.00e-02 2.50e+03 pdb=" O1 BMQ9 H 501 " -0.063 2.00e-02 2.50e+03 pdb=" O4 BMQ9 H 501 " -0.374 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C42AMQ9 B 202 " 0.264 2.00e-02 2.50e+03 2.22e-01 6.18e+02 pdb=" C43AMQ9 B 202 " -0.374 2.00e-02 2.50e+03 pdb=" C44AMQ9 B 202 " -0.077 2.00e-02 2.50e+03 pdb=" C45AMQ9 B 202 " 0.177 2.00e-02 2.50e+03 pdb=" C46AMQ9 B 202 " 0.010 2.00e-02 2.50e+03 ... (remaining 6392 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 146 2.47 - 3.08: 28190 3.08 - 3.68: 59784 3.68 - 4.29: 89304 4.29 - 4.90: 147193 Nonbonded interactions: 324617 Sorted by model distance: nonbonded pdb=" OE2 GLU F 372 " pdb="ZN ZN F 501 " model vdw 1.861 2.230 nonbonded pdb=" OG1 THR F 270 " pdb=" OE1 GLU F 273 " model vdw 1.934 3.040 nonbonded pdb=" OG SER N 341 " pdb=" OH TYR N 462 " model vdw 1.981 3.040 nonbonded pdb=" OD2 ASP H 123 " pdb=" OG SER H 187 " model vdw 2.046 3.040 nonbonded pdb=" O TRP D 90 " pdb=" OG1 THR D 91 " model vdw 2.048 3.040 ... (remaining 324612 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 38.400 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.853 36871 Z= 0.495 Angle : 0.841 49.615 50652 Z= 0.354 Chirality : 0.040 0.252 6095 Planarity : 0.008 0.222 6395 Dihedral : 11.431 158.099 12287 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.78 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.12), residues: 5021 helix: 1.37 (0.10), residues: 2833 sheet: 0.03 (0.32), residues: 270 loop : 0.05 (0.15), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 75 TYR 0.057 0.002 TYR N 367 PHE 0.022 0.001 PHE L 345 TRP 0.019 0.001 TRP I 62 HIS 0.007 0.001 HIS N 264 Details of bonding type rmsd covalent geometry : bond 0.00444 (36830) covalent geometry : angle 0.62928 (50559) hydrogen bonds : bond 0.12680 ( 2289) hydrogen bonds : angle 6.54143 ( 6624) metal coordination : bond 0.02774 ( 40) metal coordination : angle 13.04137 ( 93) Misc. bond : bond 0.85255 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.285 Fit side-chains REVERT: B 70 MET cc_start: 0.8801 (ttp) cc_final: 0.8592 (ttm) REVERT: M 152 MET cc_start: 0.8967 (ptt) cc_final: 0.8740 (ptp) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.6752 time to fit residues: 125.8923 Evaluate side-chains 151 residues out of total 3933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 0.5980 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.6980 chunk 494 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN D 186 ASN D 412 GLN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 179 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.036958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.030815 restraints weight = 265074.014| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.34 r_work: 0.2930 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 36871 Z= 0.157 Angle : 0.829 44.371 50652 Z= 0.307 Chirality : 0.042 0.180 6095 Planarity : 0.005 0.126 6395 Dihedral : 6.637 155.442 5618 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.11 % Favored : 96.75 % Rotamer: Outliers : 0.28 % Allowed : 4.10 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.12), residues: 5021 helix: 1.63 (0.10), residues: 2845 sheet: 0.12 (0.32), residues: 256 loop : 0.11 (0.15), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 257 TYR 0.032 0.002 TYR N 367 PHE 0.029 0.002 PHE L 345 TRP 0.013 0.001 TRP N 309 HIS 0.007 0.001 HIS M 357 Details of bonding type rmsd covalent geometry : bond 0.00352 (36830) covalent geometry : angle 0.59580 (50559) hydrogen bonds : bond 0.04313 ( 2289) hydrogen bonds : angle 5.18267 ( 6624) metal coordination : bond 0.01760 ( 40) metal coordination : angle 13.46389 ( 93) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 152 time to evaluate : 1.411 Fit side-chains REVERT: I 122 MET cc_start: 0.9416 (ttp) cc_final: 0.9199 (ttp) REVERT: H 48 MET cc_start: 0.9189 (mtm) cc_final: 0.8978 (mtm) REVERT: H 250 MET cc_start: 0.9371 (mmp) cc_final: 0.9142 (mmm) outliers start: 9 outliers final: 0 residues processed: 153 average time/residue: 0.7191 time to fit residues: 134.6538 Evaluate side-chains 151 residues out of total 3933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 486 optimal weight: 2.9990 chunk 424 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 189 optimal weight: 5.9990 chunk 226 optimal weight: 2.9990 chunk 480 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 390 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 59 GLN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 513 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.036023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.029809 restraints weight = 265375.144| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.20 r_work: 0.2900 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.121 36871 Z= 0.249 Angle : 0.826 46.131 50652 Z= 0.310 Chirality : 0.043 0.191 6095 Planarity : 0.005 0.126 6395 Dihedral : 6.464 156.782 5618 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.05 % Favored : 96.81 % Rotamer: Outliers : 0.59 % Allowed : 5.97 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.12), residues: 5021 helix: 1.65 (0.10), residues: 2855 sheet: 0.09 (0.32), residues: 267 loop : 0.15 (0.16), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 257 TYR 0.035 0.002 TYR G 644 PHE 0.026 0.002 PHE L 345 TRP 0.014 0.001 TRP H 299 HIS 0.008 0.001 HIS I 42 Details of bonding type rmsd covalent geometry : bond 0.00570 (36830) covalent geometry : angle 0.60618 (50559) hydrogen bonds : bond 0.04380 ( 2289) hydrogen bonds : angle 5.01281 ( 6624) metal coordination : bond 0.03156 ( 40) metal coordination : angle 13.10401 ( 93) Misc. bond : bond 0.00286 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 1.511 Fit side-chains REVERT: B 37 CYS cc_start: 0.9473 (OUTLIER) cc_final: 0.8879 (p) REVERT: C 144 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8700 (ttm) REVERT: D 422 MET cc_start: 0.9191 (mtp) cc_final: 0.8943 (mtm) REVERT: I 122 MET cc_start: 0.9341 (ttp) cc_final: 0.9102 (ttp) REVERT: H 48 MET cc_start: 0.9135 (mtm) cc_final: 0.8932 (mtm) REVERT: L 466 MET cc_start: 0.9289 (mtp) cc_final: 0.9034 (mmt) outliers start: 19 outliers final: 3 residues processed: 160 average time/residue: 0.7034 time to fit residues: 138.9673 Evaluate side-chains 156 residues out of total 3933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 151 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 52 MET Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain N residue 261 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 467 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 457 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 193 optimal weight: 6.9990 chunk 383 optimal weight: 0.0870 chunk 53 optimal weight: 3.9990 chunk 490 optimal weight: 1.9990 chunk 438 optimal weight: 2.9990 chunk 290 optimal weight: 3.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.036568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.030349 restraints weight = 264393.490| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.22 r_work: 0.2934 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 36871 Z= 0.146 Angle : 0.752 44.620 50652 Z= 0.280 Chirality : 0.040 0.167 6095 Planarity : 0.005 0.124 6395 Dihedral : 6.231 153.303 5618 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.09 % Favored : 96.79 % Rotamer: Outliers : 0.80 % Allowed : 6.96 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.12), residues: 5021 helix: 1.69 (0.10), residues: 2865 sheet: 0.08 (0.32), residues: 277 loop : 0.11 (0.16), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 700 TYR 0.024 0.001 TYR M 444 PHE 0.028 0.001 PHE L 345 TRP 0.014 0.001 TRP L 148 HIS 0.005 0.001 HIS I 42 Details of bonding type rmsd covalent geometry : bond 0.00330 (36830) covalent geometry : angle 0.54677 (50559) hydrogen bonds : bond 0.03872 ( 2289) hydrogen bonds : angle 4.84135 ( 6624) metal coordination : bond 0.01820 ( 40) metal coordination : angle 12.04933 ( 93) Misc. bond : bond 0.00099 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 1.524 Fit side-chains REVERT: C 31 MET cc_start: 0.9419 (mtp) cc_final: 0.9130 (mtp) REVERT: C 144 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8604 (ttm) REVERT: D 422 MET cc_start: 0.9140 (mtp) cc_final: 0.8900 (mtm) REVERT: G 84 MET cc_start: 0.9085 (ttm) cc_final: 0.8668 (ttm) REVERT: I 122 MET cc_start: 0.9316 (ttp) cc_final: 0.9044 (ttp) REVERT: M 135 MET cc_start: 0.9321 (tpp) cc_final: 0.8626 (tpp) outliers start: 26 outliers final: 4 residues processed: 170 average time/residue: 0.6219 time to fit residues: 130.4616 Evaluate side-chains 156 residues out of total 3933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 151 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain G residue 744 VAL Chi-restraints excluded: chain N residue 452 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 192 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 297 optimal weight: 6.9990 chunk 369 optimal weight: 10.0000 chunk 250 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 363 optimal weight: 40.0000 chunk 151 optimal weight: 1.9990 chunk 12 optimal weight: 0.0040 chunk 372 optimal weight: 20.0000 chunk 419 optimal weight: 10.0000 overall best weight: 1.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 203 HIS ** N 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.036320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.030076 restraints weight = 265720.544| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.25 r_work: 0.2922 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 36871 Z= 0.170 Angle : 0.761 44.207 50652 Z= 0.282 Chirality : 0.041 0.214 6095 Planarity : 0.005 0.123 6395 Dihedral : 6.154 152.690 5618 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.11 % Favored : 96.77 % Rotamer: Outliers : 1.14 % Allowed : 7.61 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.12), residues: 5021 helix: 1.72 (0.10), residues: 2874 sheet: 0.12 (0.32), residues: 277 loop : 0.13 (0.16), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 700 TYR 0.026 0.001 TYR G 644 PHE 0.026 0.001 PHE L 345 TRP 0.013 0.001 TRP L 148 HIS 0.006 0.001 HIS I 42 Details of bonding type rmsd covalent geometry : bond 0.00388 (36830) covalent geometry : angle 0.55344 (50559) hydrogen bonds : bond 0.03906 ( 2289) hydrogen bonds : angle 4.78531 ( 6624) metal coordination : bond 0.02250 ( 40) metal coordination : angle 12.20695 ( 93) Misc. bond : bond 0.00141 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 151 time to evaluate : 1.009 Fit side-chains REVERT: C 144 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8636 (ttm) REVERT: D 422 MET cc_start: 0.9141 (mtp) cc_final: 0.8899 (mtm) REVERT: G 84 MET cc_start: 0.9088 (ttm) cc_final: 0.8677 (ttm) REVERT: I 122 MET cc_start: 0.9293 (ttp) cc_final: 0.9004 (ttp) REVERT: M 135 MET cc_start: 0.9353 (tpp) cc_final: 0.8597 (tpp) outliers start: 37 outliers final: 13 residues processed: 175 average time/residue: 0.6206 time to fit residues: 134.2358 Evaluate side-chains 165 residues out of total 3933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain G residue 744 VAL Chi-restraints excluded: chain G residue 758 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain N residue 452 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 109 optimal weight: 10.0000 chunk 428 optimal weight: 8.9990 chunk 122 optimal weight: 0.1980 chunk 183 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 216 optimal weight: 0.8980 chunk 404 optimal weight: 4.9990 chunk 196 optimal weight: 0.7980 chunk 436 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 168 optimal weight: 0.0670 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 248 GLN N 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.036968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.030800 restraints weight = 264212.897| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.25 r_work: 0.2964 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 36871 Z= 0.113 Angle : 0.729 42.187 50652 Z= 0.266 Chirality : 0.040 0.182 6095 Planarity : 0.004 0.122 6395 Dihedral : 5.997 149.812 5618 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.95 % Favored : 96.93 % Rotamer: Outliers : 0.99 % Allowed : 8.13 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.12), residues: 5021 helix: 1.79 (0.10), residues: 2880 sheet: 0.06 (0.32), residues: 281 loop : 0.17 (0.16), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 383 TYR 0.026 0.001 TYR G 644 PHE 0.027 0.001 PHE L 345 TRP 0.013 0.001 TRP L 148 HIS 0.005 0.001 HIS M 357 Details of bonding type rmsd covalent geometry : bond 0.00248 (36830) covalent geometry : angle 0.52297 (50559) hydrogen bonds : bond 0.03578 ( 2289) hydrogen bonds : angle 4.67059 ( 6624) metal coordination : bond 0.01212 ( 40) metal coordination : angle 11.84835 ( 93) Misc. bond : bond 0.00090 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 1.257 Fit side-chains REVERT: O 29 ARG cc_start: 0.9223 (OUTLIER) cc_final: 0.8774 (mtp85) REVERT: C 144 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8544 (ttm) REVERT: D 422 MET cc_start: 0.9118 (mtp) cc_final: 0.8880 (mtm) REVERT: G 84 MET cc_start: 0.9165 (ttm) cc_final: 0.8742 (ttm) REVERT: G 401 SER cc_start: 0.8971 (OUTLIER) cc_final: 0.8743 (t) REVERT: I 122 MET cc_start: 0.9239 (ttp) cc_final: 0.8943 (ttp) REVERT: H 321 MET cc_start: 0.9470 (OUTLIER) cc_final: 0.9227 (ttp) REVERT: M 135 MET cc_start: 0.9246 (tpp) cc_final: 0.8399 (tpp) outliers start: 32 outliers final: 9 residues processed: 173 average time/residue: 0.6624 time to fit residues: 142.1736 Evaluate side-chains 164 residues out of total 3933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 29 ARG Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain G residue 401 SER Chi-restraints excluded: chain G residue 758 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 321 MET Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 263 PHE Chi-restraints excluded: chain N residue 452 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 496 optimal weight: 0.9990 chunk 242 optimal weight: 10.0000 chunk 335 optimal weight: 5.9990 chunk 346 optimal weight: 8.9990 chunk 215 optimal weight: 3.9990 chunk 311 optimal weight: 10.0000 chunk 253 optimal weight: 4.9990 chunk 449 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 423 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 556 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.035638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.029447 restraints weight = 264836.028| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.22 r_work: 0.2894 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.133 36871 Z= 0.273 Angle : 0.798 46.752 50652 Z= 0.307 Chirality : 0.043 0.195 6095 Planarity : 0.005 0.121 6395 Dihedral : 6.122 153.315 5618 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.15 % Favored : 96.73 % Rotamer: Outliers : 0.99 % Allowed : 8.75 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.12), residues: 5021 helix: 1.79 (0.10), residues: 2868 sheet: 0.22 (0.32), residues: 280 loop : 0.16 (0.16), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 162 TYR 0.040 0.002 TYR G 644 PHE 0.024 0.002 PHE L 345 TRP 0.013 0.001 TRP H 299 HIS 0.008 0.001 HIS I 42 Details of bonding type rmsd covalent geometry : bond 0.00623 (36830) covalent geometry : angle 0.60475 (50559) hydrogen bonds : bond 0.04111 ( 2289) hydrogen bonds : angle 4.77501 ( 6624) metal coordination : bond 0.03405 ( 40) metal coordination : angle 12.15062 ( 93) Misc. bond : bond 0.00220 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 1.432 Fit side-chains REVERT: C 144 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8699 (ttm) REVERT: D 300 MET cc_start: 0.9217 (mmm) cc_final: 0.8946 (mpp) REVERT: D 375 VAL cc_start: 0.9540 (OUTLIER) cc_final: 0.9340 (p) REVERT: D 422 MET cc_start: 0.9184 (mtp) cc_final: 0.8921 (mtm) REVERT: G 84 MET cc_start: 0.9076 (ttm) cc_final: 0.8671 (ttm) REVERT: G 401 SER cc_start: 0.9111 (OUTLIER) cc_final: 0.8873 (t) REVERT: I 122 MET cc_start: 0.9305 (ttp) cc_final: 0.9045 (ttp) outliers start: 32 outliers final: 14 residues processed: 173 average time/residue: 0.6822 time to fit residues: 147.0781 Evaluate side-chains 168 residues out of total 3933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 29 ARG Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 346 MET Chi-restraints excluded: chain G residue 401 SER Chi-restraints excluded: chain G residue 744 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain N residue 452 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 279 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 178 optimal weight: 0.9990 chunk 232 optimal weight: 5.9990 chunk 119 optimal weight: 0.6980 chunk 252 optimal weight: 0.9990 chunk 345 optimal weight: 2.9990 chunk 475 optimal weight: 0.0980 chunk 60 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.036778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.030604 restraints weight = 263467.078| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.23 r_work: 0.2953 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 36871 Z= 0.116 Angle : 0.730 42.812 50652 Z= 0.268 Chirality : 0.039 0.174 6095 Planarity : 0.004 0.120 6395 Dihedral : 5.992 150.820 5618 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.03 % Favored : 96.85 % Rotamer: Outliers : 0.68 % Allowed : 9.27 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.12), residues: 5021 helix: 1.81 (0.10), residues: 2877 sheet: 0.07 (0.32), residues: 281 loop : 0.21 (0.16), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 383 TYR 0.027 0.001 TYR G 644 PHE 0.027 0.001 PHE L 345 TRP 0.014 0.001 TRP N 309 HIS 0.004 0.001 HIS M 357 Details of bonding type rmsd covalent geometry : bond 0.00254 (36830) covalent geometry : angle 0.52646 (50559) hydrogen bonds : bond 0.03614 ( 2289) hydrogen bonds : angle 4.66660 ( 6624) metal coordination : bond 0.01340 ( 40) metal coordination : angle 11.81245 ( 93) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 1.489 Fit side-chains REVERT: C 144 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8577 (ttm) REVERT: D 422 MET cc_start: 0.9082 (mtp) cc_final: 0.8871 (mtm) REVERT: G 84 MET cc_start: 0.9144 (ttm) cc_final: 0.8675 (ttm) REVERT: G 401 SER cc_start: 0.9013 (OUTLIER) cc_final: 0.8773 (t) REVERT: I 122 MET cc_start: 0.9245 (ttp) cc_final: 0.8946 (ttp) REVERT: N 447 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9194 (mm) REVERT: M 135 MET cc_start: 0.9253 (tpp) cc_final: 0.8350 (tpp) outliers start: 22 outliers final: 10 residues processed: 168 average time/residue: 0.7155 time to fit residues: 149.9485 Evaluate side-chains 164 residues out of total 3933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 401 SER Chi-restraints excluded: chain G residue 758 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 263 PHE Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain N residue 447 LEU Chi-restraints excluded: chain N residue 452 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 59 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 313 optimal weight: 9.9990 chunk 271 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.036492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.030260 restraints weight = 269008.915| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.27 r_work: 0.2936 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 36871 Z= 0.149 Angle : 0.754 47.875 50652 Z= 0.274 Chirality : 0.040 0.179 6095 Planarity : 0.004 0.118 6395 Dihedral : 5.943 151.443 5618 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.05 % Favored : 96.83 % Rotamer: Outliers : 0.74 % Allowed : 9.64 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.12), residues: 5021 helix: 1.84 (0.10), residues: 2878 sheet: 0.13 (0.32), residues: 281 loop : 0.22 (0.16), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 700 TYR 0.032 0.001 TYR G 644 PHE 0.026 0.001 PHE L 345 TRP 0.012 0.001 TRP N 309 HIS 0.005 0.001 HIS I 42 Details of bonding type rmsd covalent geometry : bond 0.00341 (36830) covalent geometry : angle 0.54439 (50559) hydrogen bonds : bond 0.03684 ( 2289) hydrogen bonds : angle 4.64443 ( 6624) metal coordination : bond 0.01984 ( 40) metal coordination : angle 12.19662 ( 93) Misc. bond : bond 0.00093 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 1.403 Fit side-chains REVERT: O 29 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.8724 (mtp85) REVERT: B 91 MET cc_start: 0.9529 (mtm) cc_final: 0.9327 (mtm) REVERT: C 144 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8628 (ttm) REVERT: D 300 MET cc_start: 0.9138 (mmm) cc_final: 0.8878 (mpp) REVERT: G 84 MET cc_start: 0.9118 (ttm) cc_final: 0.8690 (ttm) REVERT: G 401 SER cc_start: 0.9024 (OUTLIER) cc_final: 0.8780 (t) REVERT: I 122 MET cc_start: 0.9227 (ttp) cc_final: 0.8961 (ttp) REVERT: H 46 MET cc_start: 0.9413 (mtt) cc_final: 0.9000 (mtt) REVERT: M 135 MET cc_start: 0.9298 (tpp) cc_final: 0.8410 (tpp) outliers start: 24 outliers final: 14 residues processed: 171 average time/residue: 0.7040 time to fit residues: 149.8661 Evaluate side-chains 168 residues out of total 3933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 29 ARG Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 401 SER Chi-restraints excluded: chain G residue 744 VAL Chi-restraints excluded: chain G residue 758 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 263 PHE Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain N residue 452 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 190 optimal weight: 4.9990 chunk 354 optimal weight: 0.7980 chunk 274 optimal weight: 0.0870 chunk 46 optimal weight: 2.9990 chunk 439 optimal weight: 0.8980 chunk 238 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 397 optimal weight: 2.9990 chunk 253 optimal weight: 4.9990 chunk 328 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.036814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.030632 restraints weight = 262913.612| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.24 r_work: 0.2958 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 36871 Z= 0.121 Angle : 0.738 47.967 50652 Z= 0.267 Chirality : 0.039 0.174 6095 Planarity : 0.004 0.118 6395 Dihedral : 5.874 150.768 5618 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.03 % Favored : 96.85 % Rotamer: Outliers : 0.80 % Allowed : 9.67 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.12), residues: 5021 helix: 1.86 (0.10), residues: 2882 sheet: 0.16 (0.32), residues: 279 loop : 0.24 (0.16), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 383 TYR 0.030 0.001 TYR G 644 PHE 0.026 0.001 PHE L 345 TRP 0.013 0.001 TRP N 309 HIS 0.004 0.001 HIS I 42 Details of bonding type rmsd covalent geometry : bond 0.00274 (36830) covalent geometry : angle 0.52906 (50559) hydrogen bonds : bond 0.03557 ( 2289) hydrogen bonds : angle 4.59758 ( 6624) metal coordination : bond 0.01506 ( 40) metal coordination : angle 12.00590 ( 93) Misc. bond : bond 0.00053 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 1.382 Fit side-chains REVERT: O 29 ARG cc_start: 0.9246 (OUTLIER) cc_final: 0.8700 (mtp85) REVERT: A 107 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7597 (m-80) REVERT: C 144 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8584 (ttm) REVERT: G 84 MET cc_start: 0.9135 (ttm) cc_final: 0.8688 (ttm) REVERT: G 401 SER cc_start: 0.8968 (OUTLIER) cc_final: 0.8723 (t) REVERT: I 122 MET cc_start: 0.9207 (ttp) cc_final: 0.8937 (ttp) REVERT: N 337 MET cc_start: 0.9297 (tmm) cc_final: 0.8698 (ttp) REVERT: M 135 MET cc_start: 0.9271 (tpp) cc_final: 0.8356 (tpp) outliers start: 26 outliers final: 14 residues processed: 170 average time/residue: 0.6770 time to fit residues: 142.1703 Evaluate side-chains 169 residues out of total 3933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 29 ARG Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 401 SER Chi-restraints excluded: chain G residue 744 VAL Chi-restraints excluded: chain G residue 758 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 263 PHE Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain N residue 452 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 473 optimal weight: 8.9990 chunk 469 optimal weight: 3.9990 chunk 165 optimal weight: 0.8980 chunk 265 optimal weight: 0.9980 chunk 171 optimal weight: 3.9990 chunk 319 optimal weight: 0.5980 chunk 133 optimal weight: 10.0000 chunk 286 optimal weight: 0.0170 chunk 26 optimal weight: 4.9990 chunk 461 optimal weight: 2.9990 chunk 235 optimal weight: 0.8980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.037048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.030891 restraints weight = 261507.800| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.26 r_work: 0.2975 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 36871 Z= 0.114 Angle : 0.730 46.701 50652 Z= 0.265 Chirality : 0.039 0.174 6095 Planarity : 0.004 0.117 6395 Dihedral : 5.779 150.028 5618 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.93 % Favored : 96.95 % Rotamer: Outliers : 0.62 % Allowed : 9.89 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.12), residues: 5021 helix: 1.91 (0.10), residues: 2883 sheet: 0.18 (0.32), residues: 282 loop : 0.29 (0.16), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 700 TYR 0.029 0.001 TYR G 644 PHE 0.026 0.001 PHE L 345 TRP 0.013 0.001 TRP L 148 HIS 0.005 0.001 HIS M 357 Details of bonding type rmsd covalent geometry : bond 0.00256 (36830) covalent geometry : angle 0.52738 (50559) hydrogen bonds : bond 0.03467 ( 2289) hydrogen bonds : angle 4.53453 ( 6624) metal coordination : bond 0.01344 ( 40) metal coordination : angle 11.80746 ( 93) Misc. bond : bond 0.00054 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13608.58 seconds wall clock time: 232 minutes 7.44 seconds (13927.44 seconds total)