Starting phenix.real_space_refine on Sun Dec 10 03:14:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdp_14664/12_2023/7zdp_14664_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdp_14664/12_2023/7zdp_14664.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdp_14664/12_2023/7zdp_14664_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdp_14664/12_2023/7zdp_14664_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdp_14664/12_2023/7zdp_14664_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdp_14664/12_2023/7zdp_14664.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdp_14664/12_2023/7zdp_14664.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdp_14664/12_2023/7zdp_14664_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdp_14664/12_2023/7zdp_14664_updated.pdb" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.012 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 1 8.98 5 Fe 28 7.16 5 Zn 1 6.06 5 P 10 5.49 5 S 466 5.16 5 C 42396 2.51 5 N 11130 2.21 5 O 11803 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "4 GLU 67": "OE1" <-> "OE2" Residue "4 PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A GLU 112": "OE1" <-> "OE2" Residue "H GLU 192": "OE1" <-> "OE2" Residue "J GLU 100": "OE1" <-> "OE2" Residue "L TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 123": "OE1" <-> "OE2" Residue "M GLU 378": "OE1" <-> "OE2" Residue "X GLU 75": "OE1" <-> "OE2" Residue "l GLU 41": "OE1" <-> "OE2" Residue "l GLU 88": "OE1" <-> "OE2" Residue "q ARG 27": "NH1" <-> "NH2" Residue "r GLU 16": "OE1" <-> "OE2" Residue "r GLU 121": "OE1" <-> "OE2" Residue "v GLU 18": "OE1" <-> "OE2" Residue "v GLU 32": "OE1" <-> "OE2" Residue "v GLU 35": "OE1" <-> "OE2" Residue "v GLU 149": "OE1" <-> "OE2" Residue "w GLU 101": "OE1" <-> "OE2" Residue "w GLU 122": "OE1" <-> "OE2" Residue "x GLU 41": "OE1" <-> "OE2" Residue "1 GLU 189": "OE1" <-> "OE2" Residue "3 TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 118": "OE1" <-> "OE2" Residue "6 TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 84": "OE1" <-> "OE2" Residue "9 GLU 164": "OE1" <-> "OE2" Residue "c GLU 27": "OE1" <-> "OE2" Residue "c GLU 90": "OE1" <-> "OE2" Residue "c GLU 97": "OE1" <-> "OE2" Residue "c GLU 107": "OE1" <-> "OE2" Residue "e GLU 37": "OE1" <-> "OE2" Residue "g GLU 64": "OE1" <-> "OE2" Residue "g GLU 88": "OE1" <-> "OE2" Residue "g GLU 108": "OE1" <-> "OE2" Residue "g GLU 110": "OE1" <-> "OE2" Residue "i GLU 2": "OE1" <-> "OE2" Residue "j GLU 61": "OE1" <-> "OE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 65835 Number of models: 1 Model: "" Number of chains: 56 Chain: "4" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3390 Classifications: {'peptide': 421} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 393} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 880 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Chain: "H" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2498 Classifications: {'peptide': 314} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 291} Chain breaks: 1 Chain: "J" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1294 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 2, 'TRANS': 166} Chain breaks: 1 Chain: "K" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 749 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 1, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 4806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4806 Classifications: {'peptide': 606} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 579} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3647 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 437} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2723 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 326} Chain: "V" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1028 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1155 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 10, 'TRANS': 128} Chain: "X" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 701 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "Y" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1403 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "Z" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1441 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "k" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2596 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain: "l" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 874 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "m" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 626 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} Chain: "n" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 634 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "o" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1004 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 10, 'TRANS': 109} Chain: "p" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1059 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 118} Chain: "q" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1142 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "r" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 846 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Chain: "s" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1047 Classifications: {'peptide': 122} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 114} Chain: "t" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1520 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 16, 'TRANS': 160} Chain: "u" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 563 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 7, 'TRANS': 57} Chain: "v" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1307 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 20, 'TRANS': 134} Chain: "w" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 846 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "x" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 412 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "y" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "z" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 576 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3312 Classifications: {'peptide': 430} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 408} Chain: "2" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1655 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 191} Chain: "3" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5275 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 32, 'TRANS': 655} Chain: "5" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1726 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "6" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "9" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1414 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "a" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 371 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "b" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 737 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "c" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1024 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "d" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2372 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain breaks: 3 Chain: "e" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "f" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 917 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 104} Chain: "g" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 969 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "h" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 769 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 11, 'TRANS': 84} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1209 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 11, 'TRANS': 133} Chain: "j" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 660 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "X" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Chain: "k" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "s" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' K': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "6" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "9" 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: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 43918 SG CYS 1 365 96.255 55.729 244.640 1.00 30.46 S ATOM 44242 SG CYS 1 405 99.211 49.891 243.874 1.00 64.99 S ATOM 43898 SG CYS 1 362 98.857 54.979 239.555 1.00 73.23 S ATOM 43879 SG CYS 1 359 103.036 54.881 244.706 1.00 28.82 S ATOM 45319 SG CYS 2 103 94.762 51.116 264.212 1.00 75.54 S ATOM 45353 SG CYS 2 108 92.621 49.286 266.165 1.00101.40 S ATOM 45633 SG CYS 2 144 95.983 47.012 260.797 1.00 95.30 S ATOM 45656 SG CYS 2 148 93.732 44.735 262.405 1.00103.70 S ATOM 46996 SG CYS 3 114 99.321 73.779 229.325 1.00 34.20 S ATOM 46935 SG CYS 3 105 94.971 77.884 231.962 1.00 46.84 S ATOM 46956 SG CYS 3 108 101.431 78.842 232.717 1.00 70.72 S ATOM 47328 SG CYS 3 156 106.831 65.521 233.836 1.00 32.75 S ATOM 47305 SG CYS 3 153 105.010 68.796 239.110 1.00 68.98 S ATOM 47352 SG CYS 3 159 111.342 69.080 237.022 1.00 73.01 S ATOM 47682 SG CYS 3 203 106.956 71.991 233.664 1.00 66.87 S ATOM 46441 SG CYS 3 41 104.531 59.087 231.839 1.00 55.21 S ATOM 46527 SG CYS 3 52 101.002 60.176 231.215 1.00101.44 S ATOM 46552 SG CYS 3 55 100.878 55.252 227.964 1.00 38.50 S ATOM 46653 SG CYS 3 69 104.469 55.012 229.117 1.00 80.11 S ATOM 53924 SG CYS 6 119 84.955 101.297 206.565 1.00 46.52 S ATOM 54154 SG CYS 6 149 82.381 99.284 212.001 1.00 61.00 S ATOM 53426 SG CYS 6 55 80.033 104.796 209.277 1.00 62.21 S ATOM 53420 SG CYS 6 54 78.458 99.266 206.834 1.00 63.08 S ATOM 55372 SG CYS 9 119 84.823 92.906 217.998 1.00 45.35 S ATOM 55346 SG CYS 9 116 87.041 99.186 218.370 1.00 50.87 S ATOM 55393 SG CYS 9 122 87.682 95.014 223.341 1.00 30.86 S ATOM 55120 SG CYS 9 87 91.132 94.286 217.772 1.00 52.49 S ATOM 55422 SG CYS 9 126 89.972 91.588 230.638 1.00 46.25 S ATOM 55093 SG CYS 9 83 93.479 92.841 225.315 1.00 23.63 S ATOM 55051 SG CYS 9 77 96.097 93.959 231.111 1.00 14.66 S ATOM 55070 SG CYS 9 80 94.692 87.706 229.087 1.00 47.83 S ATOM 56669 SG CYS b 59 92.134 87.200 246.169 1.00 87.01 S ATOM 56847 SG CYS b 84 95.236 86.741 243.826 1.00112.49 S ATOM 56869 SG CYS b 87 93.911 89.859 244.712 1.00 63.40 S Time building chain proxies: 27.65, per 1000 atoms: 0.42 Number of scatterers: 65835 At special positions: 0 Unit cell: (169.58, 203.74, 295.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 K 1 19.00 S 466 16.00 P 10 15.00 O 11803 8.00 N 11130 7.00 C 42396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS V 94 " - pdb=" SG CYS V 114 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 112 " - pdb=" SG CYS Z 124 " distance=2.03 Simple disulfide: pdb=" SG CYS l 32 " - pdb=" SG CYS l 65 " distance=2.03 Simple disulfide: pdb=" SG CYS l 42 " - pdb=" SG CYS l 55 " distance=2.04 Simple disulfide: pdb=" SG CYS s 68 " - pdb=" SG CYS s 79 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 20.67 Conformation dependent library (CDL) restraints added in 8.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 300 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 148 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 108 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 103 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 144 " pdb=" FES 3 803 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 52 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 55 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 41 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 69 " pdb=" SF4 1 501 " pdb="FE1 SF4 1 501 " - pdb=" SG CYS 1 365 " pdb="FE4 SF4 1 501 " - pdb=" SG CYS 1 359 " pdb="FE2 SF4 1 501 " - pdb=" SG CYS 1 405 " pdb="FE3 SF4 1 501 " - pdb=" SG CYS 1 362 " pdb=" SF4 3 801 " pdb="FE3 SF4 3 801 " - pdb=" NE2 HIS 3 101 " pdb="FE4 SF4 3 801 " - pdb=" SG CYS 3 108 " pdb="FE2 SF4 3 801 " - pdb=" SG CYS 3 105 " pdb="FE1 SF4 3 801 " - pdb=" SG CYS 3 114 " pdb=" SF4 3 802 " pdb="FE3 SF4 3 802 " - pdb=" SG CYS 3 159 " pdb="FE1 SF4 3 802 " - pdb=" SG CYS 3 156 " pdb="FE4 SF4 3 802 " - pdb=" SG CYS 3 203 " pdb="FE2 SF4 3 802 " - pdb=" SG CYS 3 153 " pdb=" SF4 6 300 " pdb="FE1 SF4 6 300 " - pdb=" SG CYS 6 119 " pdb="FE2 SF4 6 300 " - pdb=" SG CYS 6 149 " pdb="FE4 SF4 6 300 " - pdb=" SG CYS 6 54 " pdb="FE3 SF4 6 300 " - pdb=" SG CYS 6 55 " pdb=" SF4 9 201 " pdb="FE3 SF4 9 201 " - pdb=" SG CYS 9 122 " pdb="FE2 SF4 9 201 " - pdb=" SG CYS 9 116 " pdb="FE4 SF4 9 201 " - pdb=" SG CYS 9 87 " pdb="FE1 SF4 9 201 " - pdb=" SG CYS 9 119 " pdb=" SF4 9 202 " pdb="FE2 SF4 9 202 " - pdb=" SG CYS 9 83 " pdb="FE1 SF4 9 202 " - pdb=" SG CYS 9 126 " pdb="FE4 SF4 9 202 " - pdb=" SG CYS 9 80 " pdb="FE3 SF4 9 202 " - pdb=" SG CYS 9 77 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN b 300 " pdb="ZN ZN b 300 " - pdb=" NE2 HIS b 68 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 59 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 87 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 84 " Number of angles added : 3 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15336 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 342 helices and 29 sheets defined 51.0% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.65 Creating SS restraints... Processing helix chain '4' and resid 8 through 13 Processing helix chain '4' and resid 87 through 93 removed outlier: 4.520A pdb=" N GLU 4 92 " --> pdb=" O GLU 4 88 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR 4 93 " --> pdb=" O LYS 4 89 " (cutoff:3.500A) Processing helix chain '4' and resid 100 through 104 removed outlier: 3.968A pdb=" N ASP 4 104 " --> pdb=" O LEU 4 100 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 100 through 104' Processing helix chain '4' and resid 111 through 126 removed outlier: 4.187A pdb=" N GLU 4 115 " --> pdb=" O MET 4 111 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN 4 116 " --> pdb=" O MET 4 112 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA 4 117 " --> pdb=" O CYS 4 113 " (cutoff:3.500A) Processing helix chain '4' and resid 132 through 161 removed outlier: 3.532A pdb=" N TRP 4 136 " --> pdb=" O PRO 4 132 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU 4 147 " --> pdb=" O GLU 4 143 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE 4 151 " --> pdb=" O LEU 4 147 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET 4 152 " --> pdb=" O LEU 4 148 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR 4 156 " --> pdb=" O MET 4 152 " (cutoff:3.500A) Processing helix chain '4' and resid 165 through 184 removed outlier: 3.933A pdb=" N TRP 4 169 " --> pdb=" O THR 4 165 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE 4 171 " --> pdb=" O PHE 4 167 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU 4 172 " --> pdb=" O PHE 4 168 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU 4 173 " --> pdb=" O TRP 4 169 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU 4 179 " --> pdb=" O GLU 4 175 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE 4 180 " --> pdb=" O LYS 4 176 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR 4 181 " --> pdb=" O MET 4 177 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL 4 184 " --> pdb=" O PHE 4 180 " (cutoff:3.500A) Processing helix chain '4' and resid 207 through 227 removed outlier: 4.042A pdb=" N ASN 4 217 " --> pdb=" O GLU 4 213 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER 4 219 " --> pdb=" O SER 4 215 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU 4 220 " --> pdb=" O LYS 4 216 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG 4 221 " --> pdb=" O ASN 4 217 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE 4 222 " --> pdb=" O PHE 4 218 " (cutoff:3.500A) Processing helix chain '4' and resid 233 through 237 Processing helix chain '4' and resid 247 through 252 Processing helix chain '4' and resid 258 through 262 Processing helix chain '4' and resid 269 through 272 No H-bonds generated for 'chain '4' and resid 269 through 272' Processing helix chain '4' and resid 293 through 315 Processing helix chain '4' and resid 342 through 353 Processing helix chain '4' and resid 394 through 400 removed outlier: 3.556A pdb=" N HIS 4 398 " --> pdb=" O PRO 4 394 " (cutoff:3.500A) Processing helix chain '4' and resid 402 through 405 No H-bonds generated for 'chain '4' and resid 402 through 405' Processing helix chain '4' and resid 414 through 420 removed outlier: 3.779A pdb=" N GLY 4 419 " --> pdb=" O VAL 4 415 " (cutoff:3.500A) Processing helix chain '4' and resid 425 through 429 removed outlier: 3.817A pdb=" N ASP 4 429 " --> pdb=" O PHE 4 425 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 425 through 429' Processing helix chain 'A' and resid 2 through 22 Processing helix chain 'A' and resid 24 through 27 Processing helix chain 'A' and resid 53 through 80 Proline residue: A 74 - end of helix removed outlier: 5.820A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 Processing helix chain 'H' and resid 2 through 32 Proline residue: H 12 - end of helix Processing helix chain 'H' and resid 42 through 44 No H-bonds generated for 'chain 'H' and resid 42 through 44' Processing helix chain 'H' and resid 47 through 55 Processing helix chain 'H' and resid 68 through 86 Proline residue: H 75 - end of helix removed outlier: 4.293A pdb=" N MET H 85 " --> pdb=" O LEU H 81 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 122 removed outlier: 4.832A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 157 Processing helix chain 'H' and resid 163 through 168 removed outlier: 4.026A pdb=" N ILE H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 177 No H-bonds generated for 'chain 'H' and resid 174 through 177' Processing helix chain 'H' and resid 179 through 191 Processing helix chain 'H' and resid 217 through 242 Processing helix chain 'H' and resid 253 through 275 removed outlier: 3.539A pdb=" N ALA H 275 " --> pdb=" O LEU H 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 290 Processing helix chain 'H' and resid 293 through 310 Proline residue: H 308 - end of helix Processing helix chain 'J' and resid 2 through 21 removed outlier: 5.270A pdb=" N VAL J 6 " --> pdb=" O THR J 3 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 47 removed outlier: 3.711A pdb=" N PHE J 47 " --> pdb=" O ILE J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 58 Processing helix chain 'J' and resid 65 through 74 removed outlier: 3.678A pdb=" N MET J 74 " --> pdb=" O TYR J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 109 Processing helix chain 'J' and resid 138 through 146 removed outlier: 4.289A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 171 Processing helix chain 'K' and resid 3 through 20 Processing helix chain 'K' and resid 26 through 50 Processing helix chain 'K' and resid 55 through 83 Proline residue: K 60 - end of helix removed outlier: 5.221A pdb=" N PHE K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 23 Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 32 through 57 Proline residue: L 50 - end of helix Processing helix chain 'L' and resid 84 through 110 Proline residue: L 91 - end of helix removed outlier: 4.254A pdb=" N HIS L 109 " --> pdb=" O MET L 105 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N SER L 110 " --> pdb=" O TRP L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 132 Processing helix chain 'L' and resid 137 through 157 Processing helix chain 'L' and resid 162 through 193 Processing helix chain 'L' and resid 198 through 204 Processing helix chain 'L' and resid 210 through 223 Processing helix chain 'L' and resid 231 through 235 Processing helix chain 'L' and resid 241 through 246 Processing helix chain 'L' and resid 252 through 262 removed outlier: 4.889A pdb=" N GLY L 256 " --> pdb=" O VAL L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 269 removed outlier: 4.623A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 294 removed outlier: 4.623A pdb=" N THR L 294 " --> pdb=" O MET L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 350 removed outlier: 4.732A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 358 No H-bonds generated for 'chain 'L' and resid 356 through 358' Processing helix chain 'L' and resid 362 through 365 No H-bonds generated for 'chain 'L' and resid 362 through 365' Processing helix chain 'L' and resid 367 through 381 Processing helix chain 'L' and resid 387 through 400 removed outlier: 3.644A pdb=" N SER L 391 " --> pdb=" O THR L 387 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP L 393 " --> pdb=" O PHE L 389 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN L 400 " --> pdb=" O ILE L 396 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 430 Processing helix chain 'L' and resid 448 through 471 removed outlier: 5.114A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N PHE L 466 " --> pdb=" O LEU L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 487 No H-bonds generated for 'chain 'L' and resid 484 through 487' Processing helix chain 'L' and resid 489 through 509 Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 547 Proline residue: L 530 - end of helix removed outlier: 4.494A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N THR L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 4.507A pdb=" N THR L 543 " --> pdb=" O MET L 540 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LYS L 547 " --> pdb=" O MET L 544 " (cutoff:3.500A) Processing helix chain 'L' and resid 557 through 561 Processing helix chain 'L' and resid 563 through 577 Processing helix chain 'L' and resid 584 through 599 Processing helix chain 'M' and resid 5 through 16 Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 23 through 42 removed outlier: 4.234A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LEU M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 79 Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 109 Processing helix chain 'M' and resid 115 through 136 removed outlier: 4.387A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 140 through 170 removed outlier: 4.477A pdb=" N LEU M 143 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE M 151 " --> pdb=" O TYR M 148 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA M 155 " --> pdb=" O TYR M 152 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU M 158 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix Processing helix chain 'M' and resid 176 through 181 Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.773A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 219 No H-bonds generated for 'chain 'M' and resid 216 through 219' Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 235 through 249 removed outlier: 4.199A pdb=" N LEU M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU M 249 " --> pdb=" O ARG M 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 257 No H-bonds generated for 'chain 'M' and resid 254 through 257' Processing helix chain 'M' and resid 259 through 266 Processing helix chain 'M' and resid 268 through 278 removed outlier: 3.649A pdb=" N SER M 273 " --> pdb=" O MET M 269 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 Processing helix chain 'M' and resid 306 through 337 Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 391 through 413 removed outlier: 5.031A pdb=" N LEU M 398 " --> pdb=" O LEU M 395 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N THR M 403 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU M 408 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 447 Proline residue: M 443 - end of helix Processing helix chain 'M' and resid 451 through 453 No H-bonds generated for 'chain 'M' and resid 451 through 453' Processing helix chain 'N' and resid 3 through 22 Processing helix chain 'N' and resid 26 through 44 Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 81 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 115 through 120 removed outlier: 3.810A pdb=" N GLN N 120 " --> pdb=" O PRO N 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 132 Processing helix chain 'N' and resid 134 through 143 Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 146 through 148 No H-bonds generated for 'chain 'N' and resid 146 through 148' Processing helix chain 'N' and resid 151 through 169 Processing helix chain 'N' and resid 175 through 191 Processing helix chain 'N' and resid 198 through 222 Processing helix chain 'N' and resid 227 through 235 removed outlier: 4.922A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 Processing helix chain 'N' and resid 258 through 269 Proline residue: N 262 - end of helix Processing helix chain 'N' and resid 277 through 300 Processing helix chain 'N' and resid 310 through 315 Processing helix chain 'N' and resid 326 through 331 Processing helix chain 'N' and resid 337 through 346 Proline residue: N 341 - end of helix Processing helix chain 'V' and resid 3 through 10 Processing helix chain 'V' and resid 17 through 42 Processing helix chain 'V' and resid 48 through 80 Processing helix chain 'V' and resid 86 through 103 Processing helix chain 'V' and resid 108 through 130 Processing helix chain 'W' and resid 16 through 45 removed outlier: 4.220A pdb=" N THR W 32 " --> pdb=" O TYR W 28 " (cutoff:3.500A) Proline residue: W 35 - end of helix Processing helix chain 'W' and resid 63 through 66 Processing helix chain 'W' and resid 70 through 78 Processing helix chain 'W' and resid 83 through 117 Processing helix chain 'W' and resid 130 through 132 No H-bonds generated for 'chain 'W' and resid 130 through 132' Processing helix chain 'X' and resid 8 through 21 removed outlier: 3.530A pdb=" N LEU X 21 " --> pdb=" O TYR X 17 " (cutoff:3.500A) Processing helix chain 'X' and resid 44 through 58 Processing helix chain 'X' and resid 64 through 67 No H-bonds generated for 'chain 'X' and resid 64 through 67' Processing helix chain 'X' and resid 73 through 84 Processing helix chain 'Y' and resid 9 through 11 No H-bonds generated for 'chain 'Y' and resid 9 through 11' Processing helix chain 'Y' and resid 21 through 26 Processing helix chain 'Y' and resid 28 through 34 Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 52 through 54 No H-bonds generated for 'chain 'Y' and resid 52 through 54' Processing helix chain 'Y' and resid 56 through 74 removed outlier: 4.211A pdb=" N LEU Y 67 " --> pdb=" O ASN Y 63 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN Y 72 " --> pdb=" O GLU Y 68 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 90 Processing helix chain 'Y' and resid 96 through 98 No H-bonds generated for 'chain 'Y' and resid 96 through 98' Processing helix chain 'Y' and resid 100 through 113 Processing helix chain 'Z' and resid 28 through 39 Processing helix chain 'Z' and resid 41 through 57 Processing helix chain 'Z' and resid 73 through 75 No H-bonds generated for 'chain 'Z' and resid 73 through 75' Processing helix chain 'Z' and resid 81 through 123 removed outlier: 4.961A pdb=" N GLU Z 86 " --> pdb=" O LEU Z 82 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLU Z 118 " --> pdb=" O GLN Z 114 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N SER Z 119 " --> pdb=" O ARG Z 115 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N HIS Z 120 " --> pdb=" O GLU Z 116 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ARG Z 121 " --> pdb=" O GLY Z 117 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLN Z 122 " --> pdb=" O GLU Z 118 " (cutoff:3.500A) Processing helix chain 'Z' and resid 125 through 142 Processing helix chain 'Z' and resid 151 through 171 Processing helix chain 'k' and resid 5 through 10 Processing helix chain 'k' and resid 38 through 44 Processing helix chain 'k' and resid 58 through 62 Processing helix chain 'k' and resid 79 through 84 Processing helix chain 'k' and resid 92 through 118 Processing helix chain 'k' and resid 128 through 130 No H-bonds generated for 'chain 'k' and resid 128 through 130' Processing helix chain 'k' and resid 132 through 141 removed outlier: 3.606A pdb=" N ALA k 137 " --> pdb=" O VAL k 133 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN k 141 " --> pdb=" O ALA k 137 " (cutoff:3.500A) Processing helix chain 'k' and resid 146 through 162 removed outlier: 4.126A pdb=" N CYS k 161 " --> pdb=" O LYS k 157 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N GLU k 162 " --> pdb=" O VAL k 158 " (cutoff:3.500A) Processing helix chain 'k' and resid 176 through 186 Processing helix chain 'k' and resid 196 through 208 Processing helix chain 'k' and resid 210 through 214 Processing helix chain 'k' and resid 226 through 228 No H-bonds generated for 'chain 'k' and resid 226 through 228' Processing helix chain 'k' and resid 231 through 239 Processing helix chain 'k' and resid 253 through 263 Processing helix chain 'k' and resid 266 through 269 No H-bonds generated for 'chain 'k' and resid 266 through 269' Processing helix chain 'k' and resid 286 through 297 Processing helix chain 'k' and resid 317 through 319 No H-bonds generated for 'chain 'k' and resid 317 through 319' Processing helix chain 'l' and resid 5 through 9 Processing helix chain 'l' and resid 15 through 18 No H-bonds generated for 'chain 'l' and resid 15 through 18' Processing helix chain 'l' and resid 25 through 27 No H-bonds generated for 'chain 'l' and resid 25 through 27' Processing helix chain 'l' and resid 33 through 42 Processing helix chain 'l' and resid 48 through 54 Processing helix chain 'l' and resid 56 through 67 Processing helix chain 'l' and resid 69 through 88 Processing helix chain 'l' and resid 95 through 97 No H-bonds generated for 'chain 'l' and resid 95 through 97' Processing helix chain 'm' and resid 6 through 14 Processing helix chain 'm' and resid 16 through 34 Proline residue: m 32 - end of helix Processing helix chain 'm' and resid 38 through 46 Processing helix chain 'm' and resid 78 through 82 Processing helix chain 'n' and resid 28 through 38 Processing helix chain 'n' and resid 45 through 48 No H-bonds generated for 'chain 'n' and resid 45 through 48' Processing helix chain 'n' and resid 62 through 66 Processing helix chain 'n' and resid 70 through 86 Processing helix chain 'o' and resid 6 through 9 Processing helix chain 'o' and resid 17 through 20 Processing helix chain 'o' and resid 29 through 48 Processing helix chain 'o' and resid 58 through 96 Processing helix chain 'p' and resid 15 through 17 No H-bonds generated for 'chain 'p' and resid 15 through 17' Processing helix chain 'p' and resid 20 through 22 No H-bonds generated for 'chain 'p' and resid 20 through 22' Processing helix chain 'p' and resid 26 through 50 Processing helix chain 'p' and resid 62 through 72 Processing helix chain 'p' and resid 83 through 93 Processing helix chain 'p' and resid 95 through 116 Processing helix chain 'q' and resid 31 through 96 Proline residue: q 72 - end of helix Processing helix chain 'q' and resid 120 through 123 No H-bonds generated for 'chain 'q' and resid 120 through 123' Processing helix chain 'q' and resid 129 through 136 Processing helix chain 'r' and resid 5 through 24 Processing helix chain 'r' and resid 75 through 87 Processing helix chain 's' and resid 2 through 7 Processing helix chain 's' and resid 42 through 46 Processing helix chain 's' and resid 52 through 54 No H-bonds generated for 'chain 's' and resid 52 through 54' Processing helix chain 's' and resid 59 through 71 Processing helix chain 's' and resid 80 through 121 Processing helix chain 't' and resid 11 through 29 Processing helix chain 't' and resid 33 through 50 removed outlier: 4.072A pdb=" N HIS t 50 " --> pdb=" O ARG t 46 " (cutoff:3.500A) Processing helix chain 't' and resid 56 through 72 Processing helix chain 't' and resid 93 through 96 Processing helix chain 't' and resid 100 through 105 Processing helix chain 't' and resid 108 through 111 No H-bonds generated for 'chain 't' and resid 108 through 111' Processing helix chain 't' and resid 115 through 142 removed outlier: 5.096A pdb=" N GLU t 133 " --> pdb=" O ARG t 129 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ARG t 134 " --> pdb=" O GLU t 130 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU t 141 " --> pdb=" O LYS t 137 " (cutoff:3.500A) Processing helix chain 't' and resid 167 through 170 No H-bonds generated for 'chain 't' and resid 167 through 170' Processing helix chain 'u' and resid 19 through 42 Processing helix chain 'u' and resid 56 through 58 No H-bonds generated for 'chain 'u' and resid 56 through 58' Processing helix chain 'v' and resid 6 through 8 No H-bonds generated for 'chain 'v' and resid 6 through 8' Processing helix chain 'v' and resid 17 through 26 Processing helix chain 'v' and resid 81 through 83 No H-bonds generated for 'chain 'v' and resid 81 through 83' Processing helix chain 'v' and resid 98 through 121 Processing helix chain 'v' and resid 134 through 138 Processing helix chain 'w' and resid 37 through 40 No H-bonds generated for 'chain 'w' and resid 37 through 40' Processing helix chain 'w' and resid 51 through 64 Processing helix chain 'w' and resid 69 through 79 Processing helix chain 'w' and resid 83 through 100 removed outlier: 5.891A pdb=" N GLU w 87 " --> pdb=" O ARG w 84 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N VAL w 97 " --> pdb=" O GLU w 94 " (cutoff:3.500A) Processing helix chain 'w' and resid 115 through 117 No H-bonds generated for 'chain 'w' and resid 115 through 117' Processing helix chain 'x' and resid 14 through 46 Processing helix chain 'y' and resid 12 through 33 removed outlier: 5.187A pdb=" N VAL y 16 " --> pdb=" O HIS y 13 " (cutoff:3.500A) Proline residue: y 17 - end of helix removed outlier: 4.546A pdb=" N PHE y 22 " --> pdb=" O GLY y 19 " (cutoff:3.500A) Processing helix chain 'z' and resid 2 through 4 No H-bonds generated for 'chain 'z' and resid 2 through 4' Processing helix chain 'z' and resid 6 through 30 Proline residue: z 19 - end of helix Processing helix chain 'z' and resid 42 through 54 Processing helix chain 'z' and resid 66 through 68 No H-bonds generated for 'chain 'z' and resid 66 through 68' Processing helix chain '1' and resid 33 through 38 removed outlier: 3.507A pdb=" N SER 1 38 " --> pdb=" O LYS 1 34 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 51 Processing helix chain '1' and resid 53 through 63 Processing helix chain '1' and resid 75 through 82 removed outlier: 4.360A pdb=" N MET 1 82 " --> pdb=" O LYS 1 78 " (cutoff:3.500A) Processing helix chain '1' and resid 106 through 113 Processing helix chain '1' and resid 115 through 129 Processing helix chain '1' and resid 143 through 158 Processing helix chain '1' and resid 166 through 168 No H-bonds generated for 'chain '1' and resid 166 through 168' Processing helix chain '1' and resid 185 through 187 No H-bonds generated for 'chain '1' and resid 185 through 187' Processing helix chain '1' and resid 189 through 196 Processing helix chain '1' and resid 215 through 217 No H-bonds generated for 'chain '1' and resid 215 through 217' Processing helix chain '1' and resid 225 through 228 No H-bonds generated for 'chain '1' and resid 225 through 228' Processing helix chain '1' and resid 231 through 237 Processing helix chain '1' and resid 239 through 243 Processing helix chain '1' and resid 276 through 282 Processing helix chain '1' and resid 291 through 293 No H-bonds generated for 'chain '1' and resid 291 through 293' Processing helix chain '1' and resid 301 through 303 No H-bonds generated for 'chain '1' and resid 301 through 303' Processing helix chain '1' and resid 319 through 325 Processing helix chain '1' and resid 343 through 356 Processing helix chain '1' and resid 363 through 381 removed outlier: 4.429A pdb=" N ASP 1 370 " --> pdb=" O ARG 1 366 " (cutoff:3.500A) Processing helix chain '1' and resid 386 through 398 removed outlier: 4.035A pdb=" N ASP 1 390 " --> pdb=" O PRO 1 386 " (cutoff:3.500A) Processing helix chain '1' and resid 407 through 437 Proline residue: 1 414 - end of helix Proline residue: 1 424 - end of helix Processing helix chain '2' and resid 25 through 36 Processing helix chain '2' and resid 43 through 58 removed outlier: 4.202A pdb=" N LEU 2 48 " --> pdb=" O ALA 2 45 " (cutoff:3.500A) Proline residue: 2 49 - end of helix Processing helix chain '2' and resid 65 through 71 Processing helix chain '2' and resid 77 through 86 Processing helix chain '2' and resid 106 through 109 No H-bonds generated for 'chain '2' and resid 106 through 109' Processing helix chain '2' and resid 113 through 124 Processing helix chain '2' and resid 148 through 150 No H-bonds generated for 'chain '2' and resid 148 through 150' Processing helix chain '2' and resid 166 through 176 Processing helix chain '3' and resid 26 through 32 Processing helix chain '3' and resid 84 through 99 Processing helix chain '3' and resid 105 through 107 No H-bonds generated for 'chain '3' and resid 105 through 107' Processing helix chain '3' and resid 115 through 122 Processing helix chain '3' and resid 150 through 152 No H-bonds generated for 'chain '3' and resid 150 through 152' Processing helix chain '3' and resid 158 through 165 Processing helix chain '3' and resid 178 through 180 No H-bonds generated for 'chain '3' and resid 178 through 180' Processing helix chain '3' and resid 197 through 202 Processing helix chain '3' and resid 219 through 221 No H-bonds generated for 'chain '3' and resid 219 through 221' Processing helix chain '3' and resid 265 through 269 Processing helix chain '3' and resid 271 through 274 No H-bonds generated for 'chain '3' and resid 271 through 274' Processing helix chain '3' and resid 296 through 309 removed outlier: 3.952A pdb=" N SER 3 309 " --> pdb=" O GLY 3 305 " (cutoff:3.500A) Processing helix chain '3' and resid 312 through 314 No H-bonds generated for 'chain '3' and resid 312 through 314' Processing helix chain '3' and resid 325 through 337 Processing helix chain '3' and resid 359 through 361 No H-bonds generated for 'chain '3' and resid 359 through 361' Processing helix chain '3' and resid 369 through 372 Processing helix chain '3' and resid 384 through 387 No H-bonds generated for 'chain '3' and resid 384 through 387' Processing helix chain '3' and resid 389 through 401 Processing helix chain '3' and resid 426 through 434 removed outlier: 4.010A pdb=" N ALA 3 433 " --> pdb=" O GLN 3 430 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER 3 434 " --> pdb=" O ASP 3 431 " (cutoff:3.500A) Processing helix chain '3' and resid 438 through 444 Processing helix chain '3' and resid 457 through 459 No H-bonds generated for 'chain '3' and resid 457 through 459' Processing helix chain '3' and resid 463 through 480 Processing helix chain '3' and resid 497 through 504 removed outlier: 4.663A pdb=" N ALA 3 501 " --> pdb=" O ALA 3 497 " (cutoff:3.500A) Processing helix chain '3' and resid 512 through 516 Processing helix chain '3' and resid 534 through 536 No H-bonds generated for 'chain '3' and resid 534 through 536' Processing helix chain '3' and resid 596 through 607 Processing helix chain '3' and resid 616 through 626 Processing helix chain '3' and resid 628 through 630 No H-bonds generated for 'chain '3' and resid 628 through 630' Processing helix chain '3' and resid 642 through 649 Processing helix chain '3' and resid 668 through 670 No H-bonds generated for 'chain '3' and resid 668 through 670' Processing helix chain '3' and resid 678 through 680 No H-bonds generated for 'chain '3' and resid 678 through 680' Processing helix chain '3' and resid 682 through 691 Processing helix chain '5' and resid 17 through 32 Processing helix chain '5' and resid 54 through 66 removed outlier: 5.095A pdb=" N ILE 5 58 " --> pdb=" O ASP 5 55 " (cutoff:3.500A) Proline residue: 5 59 - end of helix Processing helix chain '5' and resid 126 through 138 removed outlier: 5.291A pdb=" N GLU 5 131 " --> pdb=" O ASN 5 128 " (cutoff:3.500A) Processing helix chain '5' and resid 207 through 209 No H-bonds generated for 'chain '5' and resid 207 through 209' Processing helix chain '6' and resid 25 through 42 Processing helix chain '6' and resid 54 through 62 Processing helix chain '6' and resid 69 through 72 Processing helix chain '6' and resid 97 through 106 Processing helix chain '6' and resid 117 through 122 Processing helix chain '6' and resid 124 through 126 No H-bonds generated for 'chain '6' and resid 124 through 126' Processing helix chain '6' and resid 136 through 138 No H-bonds generated for 'chain '6' and resid 136 through 138' Processing helix chain '6' and resid 153 through 168 Processing helix chain '6' and resid 172 through 178 Processing helix chain '9' and resid 14 through 26 Processing helix chain '9' and resid 28 through 41 Processing helix chain '9' and resid 82 through 86 Processing helix chain '9' and resid 121 through 125 Processing helix chain '9' and resid 144 through 147 Processing helix chain '9' and resid 151 through 175 removed outlier: 5.517A pdb=" N ALA 9 163 " --> pdb=" O ASP 9 159 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLU 9 164 " --> pdb=" O LYS 9 160 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ALA 9 167 " --> pdb=" O ALA 9 163 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N LEU 9 174 " --> pdb=" O GLN 9 170 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N TYR 9 175 " --> pdb=" O ALA 9 171 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 45 Processing helix chain 'a' and resid 50 through 61 removed outlier: 4.660A pdb=" N LYS a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N PHE a 61 " --> pdb=" O ASP a 57 " (cutoff:3.500A) Processing helix chain 'b' and resid 23 through 27 Processing helix chain 'b' and resid 40 through 45 Processing helix chain 'b' and resid 64 through 66 No H-bonds generated for 'chain 'b' and resid 64 through 66' Processing helix chain 'c' and resid 27 through 31 removed outlier: 4.257A pdb=" N LYS c 31 " --> pdb=" O GLU c 28 " (cutoff:3.500A) Processing helix chain 'c' and resid 89 through 98 Processing helix chain 'c' and resid 119 through 122 Processing helix chain 'd' and resid 30 through 41 removed outlier: 4.243A pdb=" N MET d 41 " --> pdb=" O HIS d 37 " (cutoff:3.500A) Processing helix chain 'd' and resid 54 through 62 removed outlier: 4.718A pdb=" N HIS d 58 " --> pdb=" O ASP d 55 " (cutoff:3.500A) Proline residue: d 61 - end of helix Processing helix chain 'd' and resid 78 through 85 Processing helix chain 'd' and resid 106 through 110 Processing helix chain 'd' and resid 112 through 123 Processing helix chain 'd' and resid 144 through 159 Processing helix chain 'd' and resid 179 through 185 removed outlier: 3.519A pdb=" N ASN d 184 " --> pdb=" O ASN d 180 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE d 185 " --> pdb=" O TYR d 181 " (cutoff:3.500A) Processing helix chain 'd' and resid 207 through 219 Processing helix chain 'd' and resid 238 through 248 Processing helix chain 'd' and resid 281 through 287 Processing helix chain 'd' and resid 301 through 303 No H-bonds generated for 'chain 'd' and resid 301 through 303' Processing helix chain 'd' and resid 310 through 312 No H-bonds generated for 'chain 'd' and resid 310 through 312' Processing helix chain 'd' and resid 314 through 318 Processing helix chain 'e' and resid 30 through 44 removed outlier: 3.607A pdb=" N LYS e 38 " --> pdb=" O ASP e 34 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TYR e 40 " --> pdb=" O ILE e 36 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL e 41 " --> pdb=" O GLU e 37 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N GLU e 42 " --> pdb=" O LYS e 38 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU e 43 " --> pdb=" O ARG e 39 " (cutoff:3.500A) Processing helix chain 'e' and resid 69 through 71 No H-bonds generated for 'chain 'e' and resid 69 through 71' Processing helix chain 'e' and resid 83 through 96 Processing helix chain 'f' and resid 19 through 36 removed outlier: 4.353A pdb=" N HIS f 36 " --> pdb=" O ASP f 32 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 59 Processing helix chain 'f' and resid 65 through 71 Processing helix chain 'f' and resid 76 through 96 Processing helix chain 'g' and resid 24 through 48 Proline residue: g 43 - end of helix Processing helix chain 'g' and resid 55 through 68 Processing helix chain 'g' and resid 75 through 93 Processing helix chain 'g' and resid 99 through 105 removed outlier: 4.714A pdb=" N PHE g 105 " --> pdb=" O HIS g 101 " (cutoff:3.500A) Processing helix chain 'g' and resid 117 through 123 Processing helix chain 'h' and resid 5 through 15 Processing helix chain 'h' and resid 53 through 55 No H-bonds generated for 'chain 'h' and resid 53 through 55' Processing helix chain 'h' and resid 59 through 61 No H-bonds generated for 'chain 'h' and resid 59 through 61' Processing helix chain 'i' and resid 3 through 17 removed outlier: 4.141A pdb=" N HIS i 17 " --> pdb=" O GLN i 13 " (cutoff:3.500A) Processing helix chain 'i' and resid 20 through 30 Processing helix chain 'i' and resid 84 through 90 removed outlier: 4.052A pdb=" N TRP i 89 " --> pdb=" O GLU i 85 " (cutoff:3.500A) Processing helix chain 'j' and resid 8 through 21 Processing helix chain 'j' and resid 44 through 58 Processing helix chain 'j' and resid 73 through 83 Processing sheet with id= A, first strand: chain '4' and resid 47 through 50 removed outlier: 3.769A pdb=" N ARG 4 63 " --> pdb=" O HIS 4 79 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYS 4 75 " --> pdb=" O GLU 4 67 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '4' and resid 361 through 368 removed outlier: 3.664A pdb=" N GLY 4 361 " --> pdb=" O SER 4 380 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER 4 380 " --> pdb=" O GLY 4 361 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'J' and resid 112 through 114 Processing sheet with id= D, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.528A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'k' and resid 122 through 125 removed outlier: 6.539A pdb=" N VAL k 168 " --> pdb=" O THR k 26 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ASP k 28 " --> pdb=" O VAL k 168 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE k 170 " --> pdb=" O ASP k 28 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLU k 219 " --> pdb=" O VAL k 169 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N TYR k 171 " --> pdb=" O GLU k 219 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU k 221 " --> pdb=" O TYR k 171 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '1' and resid 219 through 224 removed outlier: 6.303A pdb=" N ALA 1 133 " --> pdb=" O LEU 1 93 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL 1 95 " --> pdb=" O ALA 1 133 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TYR 1 135 " --> pdb=" O VAL 1 95 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ALA 1 97 " --> pdb=" O TYR 1 135 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TYR 1 137 " --> pdb=" O ALA 1 97 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASP 1 174 " --> pdb=" O ALA 1 134 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ILE 1 136 " --> pdb=" O ASP 1 174 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N PHE 1 176 " --> pdb=" O ILE 1 136 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE 1 138 " --> pdb=" O PHE 1 176 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL 1 178 " --> pdb=" O ILE 1 138 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '1' and resid 266 through 271 Processing sheet with id= H, first strand: chain '2' and resid 137 through 142 removed outlier: 6.740A pdb=" N TYR 2 98 " --> pdb=" O THR 2 138 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ILE 2 140 " --> pdb=" O TYR 2 98 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE 2 100 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL 2 142 " --> pdb=" O ILE 2 100 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL 2 102 " --> pdb=" O VAL 2 142 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N CYS 2 103 " --> pdb=" O MET 2 153 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N MET 2 153 " --> pdb=" O CYS 2 103 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '3' and resid 9 through 13 Processing sheet with id= J, first strand: chain '3' and resid 146 through 148 Processing sheet with id= K, first strand: chain '3' and resid 173 through 175 Processing sheet with id= L, first strand: chain '3' and resid 223 through 228 Processing sheet with id= M, first strand: chain '3' and resid 283 through 285 Processing sheet with id= N, first strand: chain '3' and resid 521 through 525 Processing sheet with id= O, first strand: chain '3' and resid 490 through 493 removed outlier: 7.926A pdb=" N ASN 3 491 " --> pdb=" O PRO 3 449 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL 3 451 " --> pdb=" O ASN 3 491 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU 3 493 " --> pdb=" O VAL 3 451 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU 3 453 " --> pdb=" O LEU 3 493 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL 3 376 " --> pdb=" O MET 3 450 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N VAL 3 452 " --> pdb=" O VAL 3 376 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU 3 378 " --> pdb=" O VAL 3 452 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N GLY 3 454 " --> pdb=" O LEU 3 378 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL 3 380 " --> pdb=" O GLY 3 454 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS 3 405 " --> pdb=" O VAL 3 377 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LEU 3 379 " --> pdb=" O LYS 3 405 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ALA 3 407 " --> pdb=" O LEU 3 379 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ASP 3 420 " --> pdb=" O LEU 3 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain '3' and resid 544 through 547 removed outlier: 6.454A pdb=" N VAL 3 559 " --> pdb=" O TYR 3 545 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLY 3 547 " --> pdb=" O VAL 3 559 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU 3 561 " --> pdb=" O GLY 3 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain '3' and resid 572 through 574 Processing sheet with id= R, first strand: chain '5' and resid 74 through 82 removed outlier: 6.565A pdb=" N ASN 5 95 " --> pdb=" O ALA 5 76 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU 5 78 " --> pdb=" O VAL 5 93 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL 5 93 " --> pdb=" O LEU 5 78 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA 5 80 " --> pdb=" O GLU 5 91 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLU 5 91 " --> pdb=" O ALA 5 80 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU 5 48 " --> pdb=" O ARG 5 106 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LYS 5 108 " --> pdb=" O LEU 5 48 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE 5 50 " --> pdb=" O LYS 5 108 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N TYR 5 110 " --> pdb=" O ILE 5 50 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N ILE 5 52 " --> pdb=" O TYR 5 110 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain '5' and resid 172 through 177 Processing sheet with id= T, first strand: chain '6' and resid 47 through 51 removed outlier: 6.940A pdb=" N VAL 6 85 " --> pdb=" O MET 6 48 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N PHE 6 50 " --> pdb=" O VAL 6 85 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE 6 87 " --> pdb=" O PHE 6 50 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TYR 6 112 " --> pdb=" O MET 6 86 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL 6 88 " --> pdb=" O TYR 6 112 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL 6 114 " --> pdb=" O VAL 6 88 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE 6 144 " --> pdb=" O SER 6 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain '9' and resid 65 through 67 Processing sheet with id= V, first strand: chain '9' and resid 92 through 98 removed outlier: 5.916A pdb=" N GLU 9 97 " --> pdb=" O THR 9 106 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N THR 9 106 " --> pdb=" O GLU 9 97 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'b' and resid 50 through 52 Processing sheet with id= X, first strand: chain 'b' and resid 56 through 59 Processing sheet with id= Y, first strand: chain 'c' and resid 102 through 105 Processing sheet with id= Z, first strand: chain 'c' and resid 64 through 66 Processing sheet with id= AA, first strand: chain 'd' and resid 163 through 168 removed outlier: 6.671A pdb=" N PHE d 129 " --> pdb=" O THR d 164 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILE d 166 " --> pdb=" O PHE d 129 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N HIS d 131 " --> pdb=" O ILE d 166 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N SER d 133 " --> pdb=" O PRO d 168 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLN d 44 " --> pdb=" O ALA d 21 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL d 23 " --> pdb=" O GLN d 44 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE d 46 " --> pdb=" O VAL d 23 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'e' and resid 51 through 57 removed outlier: 6.942A pdb=" N ARG e 67 " --> pdb=" O ARG e 16 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE e 18 " --> pdb=" O TRP e 65 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TRP e 65 " --> pdb=" O ILE e 18 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE e 20 " --> pdb=" O LYS e 63 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LYS e 63 " --> pdb=" O ILE e 20 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'i' and resid 60 through 63 removed outlier: 6.393A pdb=" N GLU i 50 " --> pdb=" O LEU i 38 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU i 38 " --> pdb=" O GLU i 50 " (cutoff:3.500A) 2806 hydrogen bonds defined for protein. 7824 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: 19.68 Time building geometry restraints manager: 22.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.43: 28013 1.43 - 1.65: 38656 1.65 - 1.87: 762 1.87 - 2.09: 0 2.09 - 2.31: 80 Bond restraints: 67511 Sorted by residual: bond pdb=" O2B NDP d 401 " pdb=" P2B NDP d 401 " ideal model delta sigma weight residual 1.833 1.615 0.218 3.80e-02 6.93e+02 3.30e+01 bond pdb=" C16 ZMP j 101 " pdb=" N2 ZMP j 101 " ideal model delta sigma weight residual 1.452 1.339 0.113 2.00e-02 2.50e+03 3.22e+01 bond pdb=" C13 ZMP j 101 " pdb=" N1 ZMP j 101 " ideal model delta sigma weight residual 1.451 1.339 0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" C13 ZMP X 101 " pdb=" N1 ZMP X 101 " ideal model delta sigma weight residual 1.451 1.340 0.111 2.00e-02 2.50e+03 3.09e+01 bond pdb=" C16 ZMP X 101 " pdb=" N2 ZMP X 101 " ideal model delta sigma weight residual 1.452 1.348 0.104 2.00e-02 2.50e+03 2.72e+01 ... (remaining 67506 not shown) Histogram of bond angle deviations from ideal: 69.93 - 83.34: 78 83.34 - 96.75: 9 96.75 - 110.16: 13021 110.16 - 123.57: 76223 123.57 - 136.98: 2238 Bond angle restraints: 91569 Sorted by residual: angle pdb=" O1A NAI 1 503 " pdb=" PA NAI 1 503 " pdb=" O2A NAI 1 503 " ideal model delta sigma weight residual 120.60 74.23 46.37 3.00e+00 1.11e-01 2.39e+02 angle pdb=" O1A NAI 1 503 " pdb=" PA NAI 1 503 " pdb=" O5B NAI 1 503 " ideal model delta sigma weight residual 109.30 71.11 38.19 3.00e+00 1.11e-01 1.62e+02 angle pdb=" PA NDP d 401 " pdb=" O3 NDP d 401 " pdb=" PN NDP d 401 " ideal model delta sigma weight residual 107.74 131.73 -23.99 1.95e+00 2.62e-01 1.51e+02 angle pdb=" CA PRO v 17 " pdb=" N PRO v 17 " pdb=" CD PRO v 17 " ideal model delta sigma weight residual 112.00 95.48 16.52 1.40e+00 5.10e-01 1.39e+02 angle pdb=" CA PRO p 3 " pdb=" N PRO p 3 " pdb=" CD PRO p 3 " ideal model delta sigma weight residual 112.00 96.59 15.41 1.40e+00 5.10e-01 1.21e+02 ... (remaining 91564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.32: 39139 34.32 - 68.64: 1348 68.64 - 102.96: 72 102.96 - 137.28: 4 137.28 - 171.60: 2 Dihedral angle restraints: 40565 sinusoidal: 16795 harmonic: 23770 Sorted by residual: dihedral pdb=" CA TYR 4 275 " pdb=" C TYR 4 275 " pdb=" N ASP 4 276 " pdb=" CA ASP 4 276 " ideal model delta harmonic sigma weight residual -180.00 -140.85 -39.15 0 5.00e+00 4.00e-02 6.13e+01 dihedral pdb=" CB CYS s 68 " pdb=" SG CYS s 68 " pdb=" SG CYS s 79 " pdb=" CB CYS s 79 " ideal model delta sinusoidal sigma weight residual -86.00 -146.52 60.52 1 1.00e+01 1.00e-02 4.88e+01 dihedral pdb=" C10 FMN 1 502 " pdb=" C1' FMN 1 502 " pdb=" N10 FMN 1 502 " pdb=" C2' FMN 1 502 " ideal model delta sinusoidal sigma weight residual 257.59 85.99 171.60 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 40562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.246: 10052 4.246 - 8.491: 0 8.491 - 12.737: 0 12.737 - 16.983: 0 16.983 - 21.229: 24 Chirality restraints: 10076 Sorted by residual: chirality pdb="FE3 SF4 6 300 " pdb=" S1 SF4 6 300 " pdb=" S2 SF4 6 300 " pdb=" S4 SF4 6 300 " both_signs ideal model delta sigma weight residual False -10.55 10.67 -21.23 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE4 SF4 6 300 " pdb=" S1 SF4 6 300 " pdb=" S2 SF4 6 300 " pdb=" S3 SF4 6 300 " both_signs ideal model delta sigma weight residual False 10.55 -10.62 21.18 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 9 201 " pdb=" S1 SF4 9 201 " pdb=" S2 SF4 9 201 " pdb=" S3 SF4 9 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.60 21.16 2.00e-01 2.50e+01 1.12e+04 ... (remaining 10073 not shown) Planarity restraints: 11567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR v 16 " -0.120 5.00e-02 4.00e+02 1.65e-01 4.36e+01 pdb=" N PRO v 17 " 0.285 5.00e-02 4.00e+02 pdb=" CA PRO v 17 " -0.086 5.00e-02 4.00e+02 pdb=" CD PRO v 17 " -0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA h 97 " -0.109 5.00e-02 4.00e+02 1.57e-01 3.97e+01 pdb=" N PRO h 98 " 0.272 5.00e-02 4.00e+02 pdb=" CA PRO h 98 " -0.083 5.00e-02 4.00e+02 pdb=" CD PRO h 98 " -0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 89 " 0.070 5.00e-02 4.00e+02 9.93e-02 1.58e+01 pdb=" N PRO H 90 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO H 90 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO H 90 " 0.051 5.00e-02 4.00e+02 ... (remaining 11564 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.30: 14 2.30 - 3.01: 33063 3.01 - 3.72: 122653 3.72 - 4.43: 183723 4.43 - 5.14: 310356 Nonbonded interactions: 649809 Sorted by model distance: nonbonded pdb=" N ARG q 27 " pdb=" NH2 ARG 9 32 " model vdw 1.591 3.200 nonbonded pdb=" OH TYR 1 157 " pdb=" OD1 ASP 1 174 " model vdw 2.189 2.440 nonbonded pdb=" O ILE L 556 " pdb=" OG1 THR L 560 " model vdw 2.237 2.440 nonbonded pdb=" O ILE z 26 " pdb=" OG SER z 30 " model vdw 2.287 2.440 nonbonded pdb=" O ALA N 137 " pdb=" OG SER N 140 " model vdw 2.288 2.440 ... (remaining 649804 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'X' and (resid 5 through 86 or resid 101)) selection = (chain 'j' and (resid 5 through 86 or (resid 101 and (name C10 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C3 or name C4 or name C5 o \ r name C6 or name C7 or name C8 or name C9 or name N1 or name N2 or name O1 or n \ ame O2 or name O3 or name O4 or name O5 or name O6 or name O7 or name P1 or name \ S1 )))) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 4.110 Check model and map are aligned: 0.730 Set scattering table: 0.440 Process input model: 154.470 Find NCS groups from input model: 2.000 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 165.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 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 : 0.004 0.218 67511 Z= 0.291 Angle : 0.837 46.372 91569 Z= 0.412 Chirality : 1.033 21.229 10076 Planarity : 0.006 0.165 11567 Dihedral : 16.296 171.599 25214 Min Nonbonded Distance : 1.591 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.16 % Favored : 96.83 % Rotamer: Outliers : 0.24 % Allowed : 20.75 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.09), residues: 8039 helix: -0.06 (0.07), residues: 4218 sheet: 0.31 (0.27), residues: 392 loop : -0.91 (0.10), residues: 3429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP J 125 HIS 0.006 0.001 HIS i 59 PHE 0.039 0.001 PHE K 66 TYR 0.047 0.001 TYR J 105 ARG 0.015 0.000 ARG x 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 680 time to evaluate : 5.875 Fit side-chains outliers start: 17 outliers final: 3 residues processed: 692 average time/residue: 0.6265 time to fit residues: 747.0612 Evaluate side-chains 628 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 625 time to evaluate : 5.810 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4922 time to fit residues: 10.5241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 671 optimal weight: 1.9990 chunk 602 optimal weight: 9.9990 chunk 334 optimal weight: 20.0000 chunk 205 optimal weight: 20.0000 chunk 406 optimal weight: 9.9990 chunk 321 optimal weight: 20.0000 chunk 623 optimal weight: 20.0000 chunk 241 optimal weight: 10.0000 chunk 378 optimal weight: 7.9990 chunk 463 optimal weight: 30.0000 chunk 721 optimal weight: 0.8980 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 237 ASN 4 313 GLN ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 415 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 55 HIS ** l 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 140 GLN w 36 ASN ** w 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 257 ASN 5 144 ASN 9 65 HIS c 44 ASN d 2 HIS i 122 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.0803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.262 67511 Z= 0.544 Angle : 1.573 50.979 91569 Z= 1.019 Chirality : 0.313 6.446 10076 Planarity : 0.004 0.086 11567 Dihedral : 6.510 172.009 9081 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.64 % Allowed : 19.74 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.09), residues: 8039 helix: 0.77 (0.08), residues: 4222 sheet: 0.30 (0.27), residues: 392 loop : -0.69 (0.11), residues: 3425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 272 HIS 0.009 0.001 HIS k 257 PHE 0.027 0.001 PHE N 292 TYR 0.022 0.001 TYR L 422 ARG 0.007 0.000 ARG 9 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 641 time to evaluate : 5.841 Fit side-chains revert: symmetry clash outliers start: 188 outliers final: 96 residues processed: 773 average time/residue: 0.6316 time to fit residues: 847.1180 Evaluate side-chains 715 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 619 time to evaluate : 5.785 Switching outliers to nearest non-outliers outliers start: 96 outliers final: 0 residues processed: 96 average time/residue: 0.5096 time to fit residues: 99.5535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 401 optimal weight: 6.9990 chunk 224 optimal weight: 10.0000 chunk 600 optimal weight: 20.0000 chunk 491 optimal weight: 20.0000 chunk 199 optimal weight: 5.9990 chunk 723 optimal weight: 20.0000 chunk 781 optimal weight: 0.0870 chunk 644 optimal weight: 20.0000 chunk 717 optimal weight: 20.0000 chunk 246 optimal weight: 0.0030 chunk 580 optimal weight: 5.9990 overall best weight: 3.8174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 HIS ** p 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 140 GLN u 50 HIS ** v 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 36 ASN ** w 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 99 HIS ** 6 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 44 ASN e 21 HIS i 113 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.256 67511 Z= 0.529 Angle : 1.561 50.963 91569 Z= 1.015 Chirality : 0.310 6.381 10076 Planarity : 0.004 0.064 11567 Dihedral : 6.094 171.629 9081 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.84 % Allowed : 20.14 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.10), residues: 8039 helix: 1.12 (0.08), residues: 4218 sheet: 0.33 (0.27), residues: 392 loop : -0.59 (0.11), residues: 3429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 125 HIS 0.005 0.001 HIS K 25 PHE 0.030 0.001 PHE N 292 TYR 0.023 0.001 TYR L 422 ARG 0.004 0.000 ARG x 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 649 time to evaluate : 5.883 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 131 outliers final: 55 residues processed: 757 average time/residue: 0.6428 time to fit residues: 846.7521 Evaluate side-chains 668 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 613 time to evaluate : 5.750 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 0 residues processed: 55 average time/residue: 0.5310 time to fit residues: 62.0140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 714 optimal weight: 4.9990 chunk 543 optimal weight: 20.0000 chunk 375 optimal weight: 40.0000 chunk 80 optimal weight: 20.0000 chunk 345 optimal weight: 5.9990 chunk 485 optimal weight: 8.9990 chunk 725 optimal weight: 20.0000 chunk 768 optimal weight: 4.9990 chunk 379 optimal weight: 8.9990 chunk 687 optimal weight: 20.0000 chunk 207 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 ASN N 310 ASN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 116 GLN t 140 GLN v 56 GLN v 78 HIS ** w 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 150 ASN ** 3 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 144 ASN ** 6 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 184 ASN e 79 ASN f 110 GLN ** g 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.249 67511 Z= 0.552 Angle : 1.577 51.131 91569 Z= 1.021 Chirality : 0.310 6.390 10076 Planarity : 0.004 0.057 11567 Dihedral : 5.995 171.680 9081 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.99 % Allowed : 20.98 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.10), residues: 8039 helix: 1.19 (0.08), residues: 4205 sheet: 0.21 (0.27), residues: 395 loop : -0.55 (0.11), residues: 3439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP N 167 HIS 0.009 0.001 HIS 3 437 PHE 0.027 0.001 PHE N 292 TYR 0.022 0.001 TYR L 422 ARG 0.004 0.000 ARG t 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 635 time to evaluate : 5.858 Fit side-chains revert: symmetry clash outliers start: 142 outliers final: 74 residues processed: 738 average time/residue: 0.6471 time to fit residues: 828.6383 Evaluate side-chains 681 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 607 time to evaluate : 6.004 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 0 residues processed: 74 average time/residue: 0.5078 time to fit residues: 79.2527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 639 optimal weight: 5.9990 chunk 436 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 572 optimal weight: 30.0000 chunk 317 optimal weight: 6.9990 chunk 655 optimal weight: 9.9990 chunk 531 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 392 optimal weight: 8.9990 chunk 689 optimal weight: 50.0000 chunk 193 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 235 ASN K 7 ASN ** M 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 36 ASN ** w 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.250 67511 Z= 0.535 Angle : 1.568 50.899 91569 Z= 1.017 Chirality : 0.310 6.414 10076 Planarity : 0.004 0.055 11567 Dihedral : 5.859 171.900 9081 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.25 % Allowed : 22.02 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.10), residues: 8039 helix: 1.29 (0.08), residues: 4205 sheet: 0.26 (0.27), residues: 393 loop : -0.52 (0.11), residues: 3441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP N 167 HIS 0.011 0.001 HIS 3 437 PHE 0.028 0.001 PHE N 292 TYR 0.022 0.001 TYR L 422 ARG 0.007 0.000 ARG x 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 632 time to evaluate : 5.791 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 39 residues processed: 702 average time/residue: 0.6395 time to fit residues: 777.9599 Evaluate side-chains 647 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 608 time to evaluate : 5.801 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.5456 time to fit residues: 46.8933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 258 optimal weight: 50.0000 chunk 692 optimal weight: 20.0000 chunk 151 optimal weight: 3.9990 chunk 451 optimal weight: 20.0000 chunk 189 optimal weight: 8.9990 chunk 769 optimal weight: 20.0000 chunk 638 optimal weight: 20.0000 chunk 356 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 254 optimal weight: 40.0000 chunk 403 optimal weight: 40.0000 overall best weight: 9.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 GLN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 ASN M 81 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 251 GLN ** l 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 50 HIS u 42 HIS w 36 ASN ** w 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 398 GLN ** 3 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 70 GLN ** g 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.251 67511 Z= 0.588 Angle : 1.603 51.105 91569 Z= 1.031 Chirality : 0.310 6.451 10076 Planarity : 0.004 0.061 11567 Dihedral : 6.050 172.554 9081 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.70 % Allowed : 22.23 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.10), residues: 8039 helix: 1.08 (0.08), residues: 4234 sheet: 0.16 (0.27), residues: 388 loop : -0.68 (0.11), residues: 3417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.001 TRP N 167 HIS 0.010 0.001 HIS 3 437 PHE 0.032 0.002 PHE K 66 TYR 0.022 0.002 TYR o 83 ARG 0.005 0.000 ARG x 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 632 time to evaluate : 5.864 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 121 outliers final: 63 residues processed: 709 average time/residue: 0.6388 time to fit residues: 785.0495 Evaluate side-chains 668 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 605 time to evaluate : 5.749 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.5333 time to fit residues: 69.8309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 741 optimal weight: 30.0000 chunk 86 optimal weight: 0.9990 chunk 438 optimal weight: 40.0000 chunk 561 optimal weight: 10.0000 chunk 435 optimal weight: 20.0000 chunk 647 optimal weight: 20.0000 chunk 429 optimal weight: 20.0000 chunk 766 optimal weight: 30.0000 chunk 479 optimal weight: 10.0000 chunk 467 optimal weight: 5.9990 chunk 353 optimal weight: 30.0000 overall best weight: 9.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 ASN V 88 ASN ** l 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 36 ASN ** w 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 74 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.243 67511 Z= 0.582 Angle : 1.601 50.919 91569 Z= 1.031 Chirality : 0.310 6.423 10076 Planarity : 0.004 0.065 11567 Dihedral : 6.112 173.883 9081 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.14 % Allowed : 22.98 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.10), residues: 8039 helix: 1.04 (0.08), residues: 4217 sheet: -0.05 (0.27), residues: 399 loop : -0.71 (0.11), residues: 3423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.001 TRP N 167 HIS 0.007 0.001 HIS M 30 PHE 0.027 0.001 PHE N 292 TYR 0.023 0.002 TYR o 83 ARG 0.004 0.000 ARG x 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 620 time to evaluate : 5.827 Fit side-chains revert: symmetry clash outliers start: 81 outliers final: 43 residues processed: 678 average time/residue: 0.6662 time to fit residues: 782.2274 Evaluate side-chains 641 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 598 time to evaluate : 5.785 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 1 residues processed: 43 average time/residue: 0.5263 time to fit residues: 50.1639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 474 optimal weight: 10.0000 chunk 305 optimal weight: 20.0000 chunk 457 optimal weight: 8.9990 chunk 230 optimal weight: 9.9990 chunk 150 optimal weight: 9.9990 chunk 148 optimal weight: 7.9990 chunk 487 optimal weight: 7.9990 chunk 522 optimal weight: 20.0000 chunk 378 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 602 optimal weight: 0.3980 overall best weight: 6.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 157 HIS ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 ASN ** l 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 117 HIS ** p 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 82 HIS w 36 ASN ** w 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 121 ASN e 61 GLN e 79 ASN ** h 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.252 67511 Z= 0.554 Angle : 1.589 51.158 91569 Z= 1.025 Chirality : 0.310 6.519 10076 Planarity : 0.004 0.062 11567 Dihedral : 6.027 174.027 9081 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.76 % Allowed : 23.37 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.10), residues: 8039 helix: 1.12 (0.08), residues: 4215 sheet: -0.14 (0.27), residues: 405 loop : -0.65 (0.11), residues: 3419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP N 167 HIS 0.007 0.001 HIS o 117 PHE 0.028 0.001 PHE N 292 TYR 0.023 0.001 TYR H 142 ARG 0.004 0.000 ARG t 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 614 time to evaluate : 5.797 Fit side-chains revert: symmetry clash outliers start: 54 outliers final: 26 residues processed: 652 average time/residue: 0.6523 time to fit residues: 735.6376 Evaluate side-chains 626 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 600 time to evaluate : 5.847 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 1 residues processed: 26 average time/residue: 0.5173 time to fit residues: 33.3124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 697 optimal weight: 20.0000 chunk 734 optimal weight: 30.0000 chunk 669 optimal weight: 7.9990 chunk 714 optimal weight: 7.9990 chunk 733 optimal weight: 0.0980 chunk 429 optimal weight: 20.0000 chunk 311 optimal weight: 30.0000 chunk 560 optimal weight: 6.9990 chunk 219 optimal weight: 20.0000 chunk 645 optimal weight: 20.0000 chunk 675 optimal weight: 7.9990 overall best weight: 6.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 ASN ** l 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 36 ASN ** w 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.249 67511 Z= 0.549 Angle : 1.589 50.914 91569 Z= 1.025 Chirality : 0.310 6.445 10076 Planarity : 0.004 0.060 11567 Dihedral : 5.981 173.850 9081 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.48 % Allowed : 23.73 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.10), residues: 8039 helix: 1.15 (0.08), residues: 4221 sheet: -0.13 (0.27), residues: 405 loop : -0.62 (0.11), residues: 3413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.001 TRP N 167 HIS 0.009 0.001 HIS M 30 PHE 0.028 0.001 PHE N 292 TYR 0.025 0.001 TYR H 142 ARG 0.007 0.000 ARG V 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 611 time to evaluate : 5.883 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 13 residues processed: 634 average time/residue: 0.6795 time to fit residues: 744.1580 Evaluate side-chains 613 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 600 time to evaluate : 5.910 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.5304 time to fit residues: 20.8624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 711 optimal weight: 6.9990 chunk 468 optimal weight: 0.0670 chunk 755 optimal weight: 10.0000 chunk 460 optimal weight: 2.9990 chunk 358 optimal weight: 5.9990 chunk 524 optimal weight: 20.0000 chunk 792 optimal weight: 1.9990 chunk 728 optimal weight: 8.9990 chunk 630 optimal weight: 8.9990 chunk 65 optimal weight: 50.0000 chunk 487 optimal weight: 0.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 ASN ** M 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 58 ASN ** p 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 36 ASN ** w 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 398 GLN ** 2 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.251 67511 Z= 0.528 Angle : 1.576 50.861 91569 Z= 1.020 Chirality : 0.310 6.430 10076 Planarity : 0.004 0.057 11567 Dihedral : 5.786 173.275 9081 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.20 % Allowed : 23.96 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.10), residues: 8039 helix: 1.37 (0.08), residues: 4177 sheet: 0.09 (0.27), residues: 398 loop : -0.50 (0.11), residues: 3464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP N 167 HIS 0.008 0.001 HIS M 30 PHE 0.030 0.001 PHE N 292 TYR 0.028 0.001 TYR H 142 ARG 0.004 0.000 ARG t 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 619 time to evaluate : 5.908 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 628 average time/residue: 0.6609 time to fit residues: 715.5378 Evaluate side-chains 611 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 604 time to evaluate : 5.766 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.5474 time to fit residues: 14.8048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 386 optimal weight: 0.5980 chunk 500 optimal weight: 10.0000 chunk 671 optimal weight: 7.9990 chunk 193 optimal weight: 6.9990 chunk 581 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 175 optimal weight: 8.9990 chunk 631 optimal weight: 20.0000 chunk 264 optimal weight: 6.9990 chunk 648 optimal weight: 20.0000 chunk 79 optimal weight: 7.9990 overall best weight: 6.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 ASN ** M 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 36 ASN ** w 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 437 HIS ** 6 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.065121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.057424 restraints weight = 257387.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.058738 restraints weight = 139564.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.059613 restraints weight = 90807.290| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.248 67511 Z= 0.548 Angle : 1.587 50.867 91569 Z= 1.024 Chirality : 0.310 6.429 10076 Planarity : 0.004 0.068 11567 Dihedral : 5.806 172.926 9081 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.34 % Allowed : 24.00 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.10), residues: 8039 helix: 1.30 (0.08), residues: 4196 sheet: 0.08 (0.27), residues: 398 loop : -0.54 (0.11), residues: 3445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP N 167 HIS 0.008 0.001 HIS M 30 PHE 0.028 0.001 PHE N 292 TYR 0.036 0.001 TYR H 142 ARG 0.008 0.000 ARG z 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12829.05 seconds wall clock time: 228 minutes 37.76 seconds (13717.76 seconds total)