Starting phenix.real_space_refine on Sat Dec 16 05:58:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a40_15129/12_2023/8a40_15129.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a40_15129/12_2023/8a40_15129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a40_15129/12_2023/8a40_15129.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a40_15129/12_2023/8a40_15129.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a40_15129/12_2023/8a40_15129.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a40_15129/12_2023/8a40_15129.pdb" } resolution = 3.0 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= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 11 6.06 5 P 85 5.49 5 Mg 3 5.21 5 S 212 5.16 5 C 21260 2.51 5 N 6021 2.21 5 O 6585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A ASP 540": "OD1" <-> "OD2" Residue "A TYR 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 701": "OD1" <-> "OD2" Residue "A GLU 718": "OE1" <-> "OE2" Residue "A GLU 726": "OE1" <-> "OE2" Residue "A ASP 747": "OD1" <-> "OD2" Residue "A GLU 902": "OE1" <-> "OE2" Residue "A PHE 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 927": "OE1" <-> "OE2" Residue "A GLU 951": "OE1" <-> "OE2" Residue "A GLU 1191": "OE1" <-> "OE2" Residue "A PHE 1202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1434": "OE1" <-> "OE2" Residue "B TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 62": "OE1" <-> "OE2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 34": "OD1" <-> "OD2" Residue "E ASP 70": "OD1" <-> "OD2" Residue "E GLU 78": "OE1" <-> "OE2" Residue "E ASP 177": "OD1" <-> "OD2" Residue "F GLU 84": "OE1" <-> "OE2" Residue "F GLU 86": "OE1" <-> "OE2" Residue "F ASP 88": "OD1" <-> "OD2" Residue "F TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 121": "OD1" <-> "OD2" Residue "G GLU 100": "OE1" <-> "OE2" Residue "G ASP 140": "OD1" <-> "OD2" Residue "G TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 28": "OE1" <-> "OE2" Residue "I GLU 31": "OE1" <-> "OE2" Residue "I GLU 61": "OE1" <-> "OE2" Residue "I ASP 63": "OD1" <-> "OD2" Residue "I ASP 75": "OD1" <-> "OD2" Residue "I GLU 82": "OE1" <-> "OE2" Residue "I GLU 93": "OE1" <-> "OE2" Residue "J GLU 19": "OE1" <-> "OE2" Residue "J TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 24": "OD1" <-> "OD2" Residue "K GLU 38": "OE1" <-> "OE2" Residue "K ASP 39": "OD1" <-> "OD2" Residue "K PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 93": "OD1" <-> "OD2" Residue "K GLU 102": "OE1" <-> "OE2" Residue "K ASP 111": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 34177 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 11291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1427, 11291 Classifications: {'peptide': 1427} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 68, 'TRANS': 1356} Chain breaks: 6 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 9062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1134, 9062 Classifications: {'peptide': 1134} Link IDs: {'PTRANS': 53, 'TRANS': 1080} Chain breaks: 2 Chain: "C" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1005 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "E" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1711 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1334 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "N" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 633 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain breaks: 1 Chain: "P" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 302 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 7, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 11} Chain: "T" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 827 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "U" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1343 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' MG': 3, ' ZN': 5} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 71 118.176 88.558 84.350 1.00107.72 S ATOM 486 SG CYS A 74 118.353 84.838 84.398 1.00105.48 S ATOM 533 SG CYS A 81 114.996 86.524 84.003 1.00100.06 S ATOM 768 SG CYS A 111 101.626 79.898 130.420 1.00144.34 S ATOM 796 SG CYS A 114 105.202 77.680 130.797 1.00146.37 S ATOM 1142 SG CYS A 184 103.453 80.952 132.896 1.00161.55 S ATOM 19923 SG CYS B1119 117.996 72.157 95.216 1.00105.37 S ATOM 19945 SG CYS B1122 115.643 74.492 97.110 1.00104.40 S ATOM 20060 SG CYS B1137 118.831 75.743 95.448 1.00109.04 S ATOM 20081 SG CYS B1140 118.794 73.759 98.760 1.00113.97 S ATOM 28353 SG CYS I 17 42.113 109.383 137.033 1.00122.65 S ATOM 28377 SG CYS I 20 45.649 110.794 136.288 1.00123.48 S ATOM 28538 SG CYS I 39 45.422 107.203 136.970 1.00127.75 S ATOM 28563 SG CYS I 42 44.679 109.609 139.739 1.00129.06 S ATOM 28915 SG CYS I 86 16.248 99.429 101.756 1.00105.91 S ATOM 28939 SG CYS I 89 14.807 102.569 100.301 1.00110.54 S ATOM 29143 SG CYS I 114 18.062 101.086 98.913 1.00 99.22 S ATOM 29178 SG CYS I 119 18.010 102.962 102.155 1.00106.63 S Time building chain proxies: 17.96, per 1000 atoms: 0.53 Number of scatterers: 34177 At special positions: 0 Unit cell: (181.812, 160.128, 170.136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 11 29.99 S 212 16.00 P 85 15.00 Mg 3 11.99 O 6585 8.00 N 6021 7.00 C 21260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 97 " distance=2.04 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 97 " distance=2.02 Simple disulfide: pdb=" SG CYS L 19 " - pdb=" SG CYS L 36 " distance=2.03 Simple disulfide: pdb=" SG CYS L 19 " - pdb=" SG CYS L 39 " distance=2.06 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 39 " distance=2.03 Simple disulfide: pdb=" SG CYS L 36 " - pdb=" SG CYS L 39 " distance=2.03 Simple disulfide: pdb=" SG CYS U 266 " - pdb=" SG CYS U 294 " 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=0, symmetry=0 Time building additional restraints: 15.09 Conformation dependent library (CDL) restraints added in 6.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2004 " pdb="ZN ZN A2004 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 71 " pdb=" ZN A2005 " pdb="ZN ZN A2005 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2005 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2005 " - pdb=" SG CYS A 184 " pdb=" ZN B1202 " pdb="ZN ZN B1202 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1202 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1202 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1202 " - pdb=" SG CYS B1140 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 17 " pdb=" ZN I 203 " pdb="ZN ZN I 203 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 203 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 203 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 203 " - pdb=" SG CYS I 119 " Number of angles added : 21 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7654 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 49 sheets defined 38.7% alpha, 18.4% beta 38 base pairs and 69 stacking pairs defined. Time for finding SS restraints: 12.86 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 108 removed outlier: 3.514A pdb=" N LYS A 105 " --> pdb=" O VAL A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 149 removed outlier: 3.550A pdb=" N THR A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 227 removed outlier: 3.829A pdb=" N ARG A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 244 through 249 Processing helix chain 'A' and resid 274 through 297 Processing helix chain 'A' and resid 301 through 319 removed outlier: 3.632A pdb=" N VAL A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.672A pdb=" N LEU A 438 " --> pdb=" O PRO A 435 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N HIS A 439 " --> pdb=" O SER A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 521 through 525 removed outlier: 3.528A pdb=" N ILE A 525 " --> pdb=" O PRO A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 550 removed outlier: 3.558A pdb=" N LEU A 542 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 547 " --> pdb=" O THR A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 588 through 596 Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 661 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.613A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.551A pdb=" N SER A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 759 Processing helix chain 'A' and resid 764 through 773 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 833 through 868 removed outlier: 3.817A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 removed outlier: 3.542A pdb=" N LEU A 930 " --> pdb=" O ASN A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 945 through 970 Processing helix chain 'A' and resid 971 through 974 removed outlier: 4.119A pdb=" N ASP A 974 " --> pdb=" O PRO A 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 971 through 974' Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1018 Processing helix chain 'A' and resid 1027 through 1049 removed outlier: 5.276A pdb=" N LEU A1040 " --> pdb=" O ASN A1036 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N PHE A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1079 Processing helix chain 'A' and resid 1086 through 1101 Proline residue: A1098 - end of helix removed outlier: 3.886A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1130 Processing helix chain 'A' and resid 1144 through 1149 Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1166 through 1169 No H-bonds generated for 'chain 'A' and resid 1166 through 1169' Processing helix chain 'A' and resid 1189 through 1195 removed outlier: 3.605A pdb=" N ASN A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1199 No H-bonds generated for 'chain 'A' and resid 1197 through 1199' Processing helix chain 'A' and resid 1217 through 1225 removed outlier: 3.542A pdb=" N ASP A1223 " --> pdb=" O LYS A1219 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG A1224 " --> pdb=" O HIS A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1240 removed outlier: 3.839A pdb=" N PHE A1239 " --> pdb=" O ILE A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1296 removed outlier: 3.529A pdb=" N ASN A1291 " --> pdb=" O CYS A1287 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR A1294 " --> pdb=" O SER A1290 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N MET A1296 " --> pdb=" O MET A1292 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1349 Processing helix chain 'A' and resid 1361 through 1370 Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 4.010A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1431 removed outlier: 3.737A pdb=" N SER A1431 " --> pdb=" O LEU A1427 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1446 removed outlier: 3.557A pdb=" N LEU A1439 " --> pdb=" O THR A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1453 through 1460 Processing helix chain 'A' and resid 1478 through 1482 removed outlier: 3.509A pdb=" N LYS A1481 " --> pdb=" O GLU A1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 37 Processing helix chain 'B' and resid 40 through 62 removed outlier: 4.735A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 246 through 253 removed outlier: 3.685A pdb=" N ALA B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B 252 " --> pdb=" O LYS B 248 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.703A pdb=" N HIS B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 299 removed outlier: 4.456A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 294 through 299' Processing helix chain 'B' and resid 301 through 308 Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 331 through 345 removed outlier: 3.525A pdb=" N ARG B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 357 through 377 removed outlier: 3.625A pdb=" N TYR B 363 " --> pdb=" O THR B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 424 removed outlier: 3.881A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 437 through 451 Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 495 through 500 removed outlier: 4.186A pdb=" N ARG B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.523A pdb=" N TRP B 506 " --> pdb=" O ASN B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 557 through 562 removed outlier: 3.534A pdb=" N ILE B 561 " --> pdb=" O PRO B 558 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA B 562 " --> pdb=" O ALA B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 594 Processing helix chain 'B' and resid 636 through 645 Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 667 through 671 removed outlier: 3.631A pdb=" N GLU B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 through 671' Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.716A pdb=" N LEU B 704 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 711 removed outlier: 3.847A pdb=" N ILE B 710 " --> pdb=" O CYS B 707 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE B 711 " --> pdb=" O ALA B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 removed outlier: 3.569A pdb=" N ASN B 717 " --> pdb=" O PRO B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 730 through 732 No H-bonds generated for 'chain 'B' and resid 730 through 732' Processing helix chain 'B' and resid 763 through 768 Processing helix chain 'B' and resid 798 through 802 Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.721A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 4.066A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.723A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1058 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1152 through 1164 Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.866A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.915A pdb=" N CYS C 88 " --> pdb=" O SER C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.631A pdb=" N TRP C 203 " --> pdb=" O PRO C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 271 removed outlier: 3.917A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 90 Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 removed outlier: 3.654A pdb=" N GLU D 119 " --> pdb=" O PRO D 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 116 through 119' Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 3 through 24 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 83 through 97 Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.603A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 137 removed outlier: 3.543A pdb=" N LEU E 136 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 133 through 137' Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'I' and resid 63 through 68 removed outlier: 3.558A pdb=" N ILE I 68 " --> pdb=" O LEU I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.767A pdb=" N SER I 73 " --> pdb=" O ALA I 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 27 removed outlier: 4.604A pdb=" N ALA J 20 " --> pdb=" O ASN J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.658A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.686A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 51 removed outlier: 4.124A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'U' and resid 138 through 153 Processing helix chain 'U' and resid 156 through 162 Processing helix chain 'U' and resid 164 through 181 Processing helix chain 'U' and resid 184 through 200 Processing helix chain 'U' and resid 203 through 212 removed outlier: 4.133A pdb=" N ARG U 207 " --> pdb=" O ASN U 203 " (cutoff:3.500A) Processing helix chain 'U' and resid 216 through 222 removed outlier: 3.758A pdb=" N ARG U 222 " --> pdb=" O ASP U 218 " (cutoff:3.500A) Processing helix chain 'U' and resid 231 through 249 removed outlier: 3.644A pdb=" N ARG U 246 " --> pdb=" O LYS U 242 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU U 247 " --> pdb=" O GLU U 243 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 16 removed outlier: 4.621A pdb=" N ARG B1150 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 94 removed outlier: 7.093A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 194 removed outlier: 4.362A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 264 through 266 Processing sheet with id=AA6, first strand: chain 'A' and resid 329 through 331 removed outlier: 4.506A pdb=" N LYS A 331 " --> pdb=" O ARG A 334 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AA8, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 3.668A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU A 477 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL A 380 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.873A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AB2, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.400A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ARG H 111 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLY H 101 " --> pdb=" O ARG H 111 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N SER H 113 " --> pdb=" O ILE H 99 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE H 99 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N TYR H 115 " --> pdb=" O TYR H 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.803A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB5, first strand: chain 'A' and resid 792 through 793 Processing sheet with id=AB6, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.746A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB8, first strand: chain 'A' and resid 1308 through 1310 removed outlier: 3.553A pdb=" N GLU A1337 " --> pdb=" O TYR A1308 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS A1310 " --> pdb=" O ILE A1335 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A1335 " --> pdb=" O HIS A1310 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 6.762A pdb=" N THR A1164 " --> pdb=" O LEU A1298 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1244 through 1247 removed outlier: 7.103A pdb=" N LEU A1211 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ILE A1175 " --> pdb=" O LEU A1211 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ARG A1213 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N THR A1173 " --> pdb=" O ARG A1213 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLU A1215 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AC3, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.643A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.643A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN G 53 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LYS G 71 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ILE G 51 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LYS G 73 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N PHE G 77 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N VAL G 45 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 65 through 67 removed outlier: 5.154A pdb=" N TYR B 84 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ILE B 133 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LEU B 86 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N THR B 131 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA B 122 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY B 150 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU B 124 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE B 148 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N VAL B 126 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 146 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AC7, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC8, first strand: chain 'B' and resid 391 through 394 removed outlier: 3.648A pdb=" N ALA B 196 " --> pdb=" O ARG B 484 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 206 through 208 removed outlier: 3.575A pdb=" N ILE B 235 " --> pdb=" O CYS B 221 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AD2, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AD3, first strand: chain 'B' and resid 551 through 552 removed outlier: 7.117A pdb=" N ILE B 567 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE B 576 " --> pdb=" O THR B 565 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR B 565 " --> pdb=" O ILE B 576 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 747 through 751 removed outlier: 5.980A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 747 through 751 removed outlier: 5.980A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD7, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 6.940A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AD9, first strand: chain 'B' and resid 865 through 867 removed outlier: 3.645A pdb=" N ILE B 866 " --> pdb=" O THR B 894 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 1127 through 1128 Processing sheet with id=AE2, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.560A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU C 234 " --> pdb=" O GLY C 181 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLY C 181 " --> pdb=" O GLU C 234 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.845A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.561A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 60 through 62 removed outlier: 3.894A pdb=" N VAL E 60 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL E 74 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU E 128 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.520A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 56 through 57 Processing sheet with id=AE8, first strand: chain 'G' and resid 149 through 153 removed outlier: 3.750A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU G 100 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N VAL G 89 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL G 85 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU G 145 " --> pdb=" O VAL G 85 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG G 144 " --> pdb=" O GLY G 169 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 118 through 120 removed outlier: 3.530A pdb=" N LYS G 129 " --> pdb=" O GLU G 118 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS G 127 " --> pdb=" O ASP G 120 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 24 through 29 removed outlier: 3.683A pdb=" N ILE I 34 " --> pdb=" O ASP I 29 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF3, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.761A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'U' and resid 271 through 274 removed outlier: 4.047A pdb=" N VAL U 289 " --> pdb=" O TRP U 298 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP U 298 " --> pdb=" O VAL U 289 " (cutoff:3.500A) 1402 hydrogen bonds defined for protein. 3912 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 100 hydrogen bonds 196 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 69 stacking parallelities Total time for adding SS restraints: 20.32 Time building geometry restraints manager: 15.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10805 1.34 - 1.46: 7691 1.46 - 1.58: 15982 1.58 - 1.71: 166 1.71 - 1.83: 334 Bond restraints: 34978 Sorted by residual: bond pdb=" C PRO B 81 " pdb=" N PRO B 82 " ideal model delta sigma weight residual 1.331 1.369 -0.038 1.28e-02 6.10e+03 8.66e+00 bond pdb=" CA GLU I 105 " pdb=" CB GLU I 105 " ideal model delta sigma weight residual 1.517 1.564 -0.047 2.41e-02 1.72e+03 3.86e+00 bond pdb=" C3' G P 36 " pdb=" O3' G P 36 " ideal model delta sigma weight residual 1.427 1.453 -0.026 1.50e-02 4.44e+03 3.08e+00 bond pdb=" C ARG H 81 " pdb=" N PRO H 82 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.91e+00 bond pdb=" CA THR A 832 " pdb=" C THR A 832 " ideal model delta sigma weight residual 1.525 1.561 -0.036 2.10e-02 2.27e+03 2.87e+00 ... (remaining 34973 not shown) Histogram of bond angle deviations from ideal: 96.40 - 104.91: 1002 104.91 - 113.41: 19472 113.41 - 121.92: 19810 121.92 - 130.43: 7163 130.43 - 138.94: 159 Bond angle restraints: 47606 Sorted by residual: angle pdb=" C GLN A 539 " pdb=" CA GLN A 539 " pdb=" CB GLN A 539 " ideal model delta sigma weight residual 116.63 109.35 7.28 1.16e+00 7.43e-01 3.94e+01 angle pdb=" CA GLN A 539 " pdb=" C GLN A 539 " pdb=" N ASP A 540 " ideal model delta sigma weight residual 119.63 115.30 4.33 8.10e-01 1.52e+00 2.85e+01 angle pdb=" N GLU E 96 " pdb=" CA GLU E 96 " pdb=" CB GLU E 96 " ideal model delta sigma weight residual 110.20 118.12 -7.92 1.49e+00 4.50e-01 2.83e+01 angle pdb=" C PRO K 79 " pdb=" N ASP K 80 " pdb=" CA ASP K 80 " ideal model delta sigma weight residual 126.32 135.51 -9.19 1.74e+00 3.30e-01 2.79e+01 angle pdb=" CA MET A1262 " pdb=" CB MET A1262 " pdb=" CG MET A1262 " ideal model delta sigma weight residual 114.10 123.80 -9.70 2.00e+00 2.50e-01 2.35e+01 ... (remaining 47601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 20643 35.92 - 71.85: 577 71.85 - 107.77: 36 107.77 - 143.69: 0 143.69 - 179.62: 4 Dihedral angle restraints: 21260 sinusoidal: 9431 harmonic: 11829 Sorted by residual: dihedral pdb=" CB CYS L 36 " pdb=" SG CYS L 36 " pdb=" SG CYS L 39 " pdb=" CB CYS L 39 " ideal model delta sinusoidal sigma weight residual 93.00 4.38 88.62 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS C 90 " pdb=" SG CYS C 90 " pdb=" SG CYS C 97 " pdb=" CB CYS C 97 " ideal model delta sinusoidal sigma weight residual 93.00 -179.04 -87.96 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CB CYS L 19 " pdb=" SG CYS L 19 " pdb=" SG CYS L 39 " pdb=" CB CYS L 39 " ideal model delta sinusoidal sigma weight residual -86.00 -171.06 85.06 1 1.00e+01 1.00e-02 8.77e+01 ... (remaining 21257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 5054 0.105 - 0.210: 266 0.210 - 0.315: 7 0.315 - 0.419: 0 0.419 - 0.524: 1 Chirality restraints: 5328 Sorted by residual: chirality pdb=" CB ILE A 621 " pdb=" CA ILE A 621 " pdb=" CG1 ILE A 621 " pdb=" CG2 ILE A 621 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.52 2.00e-01 2.50e+01 6.87e+00 chirality pdb=" C3' G P 36 " pdb=" C4' G P 36 " pdb=" O3' G P 36 " pdb=" C2' G P 36 " both_signs ideal model delta sigma weight residual False -2.74 -2.48 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C3' G P 38 " pdb=" C4' G P 38 " pdb=" O3' G P 38 " pdb=" C2' G P 38 " both_signs ideal model delta sigma weight residual False -2.48 -2.22 -0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 5325 not shown) Planarity restraints: 5878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 244 " -0.043 5.00e-02 4.00e+02 6.49e-02 6.73e+00 pdb=" N PRO A 245 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS U 252 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.58e+00 pdb=" C LYS U 252 " -0.044 2.00e-02 2.50e+03 pdb=" O LYS U 252 " 0.017 2.00e-02 2.50e+03 pdb=" N THR U 253 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP K 93 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.75e+00 pdb=" CG ASP K 93 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASP K 93 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP K 93 " -0.015 2.00e-02 2.50e+03 ... (remaining 5875 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 457 2.66 - 3.22: 29844 3.22 - 3.78: 53256 3.78 - 4.34: 73482 4.34 - 4.90: 119393 Nonbonded interactions: 276432 Sorted by model distance: nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2006 " model vdw 2.105 2.170 nonbonded pdb=" O ASN B1120 " pdb="ZN ZN B1201 " model vdw 2.121 2.230 nonbonded pdb=" O LEU B1121 " pdb="ZN ZN B1201 " model vdw 2.125 2.230 nonbonded pdb=" O SER I 51 " pdb="ZN ZN A2007 " model vdw 2.127 2.230 nonbonded pdb=" O3' U P 46 " pdb="MG MG A2006 " model vdw 2.135 2.170 ... (remaining 276427 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 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: 0.040 Extract box with map and model: 8.070 Check model and map are aligned: 0.530 Set scattering table: 0.340 Process input model: 112.820 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.130 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:12.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 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 0.049 34978 Z= 0.273 Angle : 0.725 13.935 47606 Z= 0.391 Chirality : 0.050 0.524 5328 Planarity : 0.005 0.075 5878 Dihedral : 15.654 179.617 13582 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.00 % 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: -0.65 (0.13), residues: 4022 helix: -0.15 (0.13), residues: 1434 sheet: 0.18 (0.21), residues: 618 loop : -0.76 (0.13), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1210 HIS 0.008 0.001 HIS A 804 PHE 0.022 0.002 PHE E 73 TYR 0.040 0.002 TYR B1048 ARG 0.021 0.001 ARG B 638 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 400 time to evaluate : 3.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 3 residues processed: 400 average time/residue: 1.6115 time to fit residues: 768.3077 Evaluate side-chains 308 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 305 time to evaluate : 4.089 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 2 average time/residue: 1.2183 time to fit residues: 8.4937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 9.9990 chunk 309 optimal weight: 0.9990 chunk 171 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 208 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 319 optimal weight: 10.0000 chunk 123 optimal weight: 4.9990 chunk 194 optimal weight: 9.9990 chunk 238 optimal weight: 0.9990 chunk 370 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 330 GLN A 341 GLN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 ASN A1093 GLN ** A1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN F 46 GLN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 GLN I 22 ASN I 84 HIS K 113 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 34978 Z= 0.364 Angle : 0.621 10.886 47606 Z= 0.327 Chirality : 0.046 0.264 5328 Planarity : 0.004 0.047 5878 Dihedral : 14.108 179.993 5387 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.12 % Allowed : 7.84 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.00 % 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: 0.04 (0.13), residues: 4022 helix: 0.82 (0.14), residues: 1453 sheet: 0.22 (0.21), residues: 623 loop : -0.59 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 27 HIS 0.007 0.001 HIS B 387 PHE 0.020 0.002 PHE U 261 TYR 0.017 0.002 TYR C 231 ARG 0.010 0.001 ARG I 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 330 time to evaluate : 3.835 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 14 residues processed: 349 average time/residue: 1.5269 time to fit residues: 638.6131 Evaluate side-chains 309 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 295 time to evaluate : 3.994 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 10 residues processed: 5 average time/residue: 0.9429 time to fit residues: 11.4967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 308 optimal weight: 4.9990 chunk 252 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 371 optimal weight: 7.9990 chunk 400 optimal weight: 20.0000 chunk 330 optimal weight: 50.0000 chunk 368 optimal weight: 6.9990 chunk 126 optimal weight: 0.0060 chunk 297 optimal weight: 0.3980 overall best weight: 3.2802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 GLN K 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 34978 Z= 0.272 Angle : 0.573 11.516 47606 Z= 0.299 Chirality : 0.044 0.219 5328 Planarity : 0.004 0.063 5878 Dihedral : 14.093 179.394 5387 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.60 % Allowed : 9.63 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.00 % 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: 0.30 (0.13), residues: 4022 helix: 1.20 (0.14), residues: 1453 sheet: 0.10 (0.20), residues: 626 loop : -0.47 (0.14), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 27 HIS 0.005 0.001 HIS A 809 PHE 0.017 0.001 PHE U 220 TYR 0.014 0.001 TYR A 413 ARG 0.006 0.000 ARG U 246 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 313 time to evaluate : 4.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 20 residues processed: 344 average time/residue: 1.5877 time to fit residues: 656.0918 Evaluate side-chains 308 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 288 time to evaluate : 3.964 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 17 residues processed: 4 average time/residue: 0.8039 time to fit residues: 9.6869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 0.9980 chunk 279 optimal weight: 9.9990 chunk 192 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 177 optimal weight: 9.9990 chunk 249 optimal weight: 9.9990 chunk 372 optimal weight: 2.9990 chunk 394 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 353 optimal weight: 10.0000 chunk 106 optimal weight: 0.0010 overall best weight: 2.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 GLN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1251 ASN ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 GLN K 113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 34978 Z= 0.251 Angle : 0.554 10.477 47606 Z= 0.288 Chirality : 0.043 0.335 5328 Planarity : 0.004 0.040 5878 Dihedral : 14.077 178.753 5387 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.79 % Allowed : 10.52 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.00 % 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 (0.13), residues: 4022 helix: 1.40 (0.14), residues: 1448 sheet: 0.10 (0.20), residues: 631 loop : -0.44 (0.14), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 27 HIS 0.004 0.001 HIS A 809 PHE 0.014 0.001 PHE C 63 TYR 0.018 0.001 TYR F 115 ARG 0.007 0.000 ARG U 246 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 309 time to evaluate : 4.398 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 26 residues processed: 345 average time/residue: 1.5364 time to fit residues: 639.4734 Evaluate side-chains 310 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 284 time to evaluate : 3.956 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 21 residues processed: 7 average time/residue: 0.8319 time to fit residues: 13.0810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 30.0000 chunk 223 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 293 optimal weight: 1.9990 chunk 162 optimal weight: 9.9990 chunk 336 optimal weight: 20.0000 chunk 272 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 9.9990 chunk 353 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 GLN A 982 ASN ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1021 HIS G 53 ASN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 GLN K 113 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 34978 Z= 0.278 Angle : 0.569 10.434 47606 Z= 0.295 Chirality : 0.044 0.302 5328 Planarity : 0.004 0.044 5878 Dihedral : 14.065 179.112 5387 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.83 % Favored : 96.15 % Rotamer: Outliers : 1.60 % Allowed : 12.06 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.00 % 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 (0.13), residues: 4022 helix: 1.43 (0.14), residues: 1452 sheet: 0.15 (0.21), residues: 622 loop : -0.42 (0.14), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 27 HIS 0.005 0.001 HIS I 100 PHE 0.033 0.001 PHE A 458 TYR 0.018 0.001 TYR F 115 ARG 0.007 0.000 ARG L 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 300 time to evaluate : 4.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 28 residues processed: 337 average time/residue: 1.5538 time to fit residues: 634.3753 Evaluate side-chains 316 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 288 time to evaluate : 4.055 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 22 residues processed: 8 average time/residue: 0.9067 time to fit residues: 15.2723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 3.9990 chunk 355 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 231 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 394 optimal weight: 0.9990 chunk 327 optimal weight: 5.9990 chunk 182 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 207 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 982 ASN ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1021 HIS G 53 ASN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 34978 Z= 0.231 Angle : 0.558 10.368 47606 Z= 0.288 Chirality : 0.043 0.351 5328 Planarity : 0.003 0.037 5878 Dihedral : 14.046 179.921 5387 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.88 % Favored : 96.10 % Rotamer: Outliers : 1.37 % Allowed : 13.32 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.00 % 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: 0.54 (0.14), residues: 4022 helix: 1.49 (0.14), residues: 1451 sheet: 0.18 (0.21), residues: 620 loop : -0.40 (0.14), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 27 HIS 0.004 0.001 HIS A 84 PHE 0.017 0.001 PHE A 458 TYR 0.017 0.001 TYR F 115 ARG 0.006 0.000 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 297 time to evaluate : 3.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 28 residues processed: 333 average time/residue: 1.5510 time to fit residues: 621.1552 Evaluate side-chains 314 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 286 time to evaluate : 4.003 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 25 residues processed: 6 average time/residue: 1.0231 time to fit residues: 13.2971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 224 optimal weight: 0.7980 chunk 288 optimal weight: 20.0000 chunk 223 optimal weight: 20.0000 chunk 332 optimal weight: 5.9990 chunk 220 optimal weight: 7.9990 chunk 393 optimal weight: 30.0000 chunk 246 optimal weight: 10.0000 chunk 239 optimal weight: 9.9990 chunk 181 optimal weight: 10.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 HIS A 982 ASN ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1021 HIS ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 34978 Z= 0.398 Angle : 0.623 10.769 47606 Z= 0.322 Chirality : 0.046 0.350 5328 Planarity : 0.004 0.046 5878 Dihedral : 14.119 179.268 5387 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.15 % Favored : 95.82 % Rotamer: Outliers : 1.54 % Allowed : 14.19 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.00 % 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: 0.42 (0.13), residues: 4022 helix: 1.40 (0.14), residues: 1441 sheet: 0.09 (0.20), residues: 625 loop : -0.46 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 27 HIS 0.006 0.001 HIS A 84 PHE 0.021 0.002 PHE A 458 TYR 0.018 0.001 TYR A 875 ARG 0.016 0.000 ARG L 37 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 295 time to evaluate : 4.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 31 residues processed: 335 average time/residue: 1.5360 time to fit residues: 622.1515 Evaluate side-chains 311 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 280 time to evaluate : 3.842 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 26 residues processed: 7 average time/residue: 0.7514 time to fit residues: 12.8299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.3213 > 50: distance: 58 - 82: 34.867 distance: 61 - 79: 25.019 distance: 73 - 79: 26.085 distance: 79 - 80: 13.136 distance: 80 - 81: 9.378 distance: 80 - 83: 13.967 distance: 81 - 82: 23.424 distance: 81 - 87: 30.810 distance: 83 - 84: 20.423 distance: 83 - 85: 11.945 distance: 84 - 86: 30.101 distance: 87 - 88: 25.028 distance: 88 - 89: 8.558 distance: 88 - 91: 9.540 distance: 89 - 93: 56.229 distance: 91 - 92: 33.158 distance: 93 - 94: 3.643 distance: 94 - 95: 36.076 distance: 94 - 97: 11.076 distance: 95 - 96: 40.084 distance: 95 - 101: 38.702 distance: 97 - 98: 33.518 distance: 98 - 99: 23.773 distance: 98 - 100: 6.836 distance: 101 - 102: 6.835 distance: 102 - 103: 9.553 distance: 102 - 105: 40.916 distance: 103 - 104: 5.494 distance: 103 - 107: 33.887 distance: 105 - 106: 28.146 distance: 107 - 108: 3.018 distance: 107 - 113: 52.583 distance: 108 - 111: 24.543 distance: 109 - 114: 56.299 distance: 111 - 112: 14.676 distance: 112 - 113: 29.550 distance: 115 - 116: 38.428 distance: 115 - 118: 29.889 distance: 116 - 117: 42.727 distance: 116 - 125: 4.021 distance: 118 - 119: 6.440 distance: 120 - 121: 31.347 distance: 121 - 122: 29.216 distance: 122 - 123: 9.129 distance: 122 - 124: 10.868 distance: 125 - 126: 23.383 distance: 126 - 127: 11.911 distance: 126 - 129: 25.439 distance: 127 - 128: 40.578 distance: 127 - 132: 23.127 distance: 129 - 130: 17.995 distance: 129 - 131: 5.967 distance: 132 - 133: 5.415 distance: 133 - 134: 13.163 distance: 133 - 136: 12.570 distance: 134 - 135: 11.455 distance: 134 - 140: 21.775 distance: 136 - 137: 11.140 distance: 136 - 138: 48.265 distance: 137 - 139: 46.476 distance: 140 - 141: 41.732 distance: 140 - 146: 33.407 distance: 141 - 142: 41.988 distance: 141 - 144: 26.430 distance: 142 - 143: 21.837 distance: 142 - 147: 29.437 distance: 144 - 145: 39.516 distance: 145 - 146: 45.132 distance: 147 - 148: 13.667 distance: 148 - 149: 23.477 distance: 148 - 151: 12.662 distance: 149 - 150: 9.244 distance: 149 - 154: 22.980 distance: 151 - 152: 24.700 distance: 151 - 153: 35.698