Starting phenix.real_space_refine on Sat Dec 16 15:58:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wau_37405/12_2023/8wau_37405_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wau_37405/12_2023/8wau_37405.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wau_37405/12_2023/8wau_37405_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wau_37405/12_2023/8wau_37405_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wau_37405/12_2023/8wau_37405_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wau_37405/12_2023/8wau_37405.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wau_37405/12_2023/8wau_37405.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wau_37405/12_2023/8wau_37405_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wau_37405/12_2023/8wau_37405_trim_updated.pdb" } resolution = 2.78 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= 0.004 sd= 0.125 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 Zn 8 6.06 5 P 113 5.49 5 Mg 1 5.21 5 S 203 5.16 5 C 22150 2.51 5 N 6272 2.21 5 O 6951 1.98 5 H 23 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "o TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 1395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 35721 Number of models: 1 Model: "" Number of chains: 25 Chain: "N" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 87 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Planarities with less than four sites: {'CSX:plan-1': 1, 'HYP:plan-1': 1, 'ILX:plan-1': 1, 'TRX:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1138 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain breaks: 1 Chain: "T" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 789 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain breaks: 1 Chain: "X" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 878 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain breaks: 1 Chain: "Y" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1112 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain: "Z" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 241 Unusual residues: {'ATP': 1} Classifications: {'RNA': 10, 'undetermined': 1} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 6} Link IDs: {'rna3p': 9, None: 1} Not linked: pdbres="ATP Z 1 " pdbres=" U Z 2 " Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Chain: "o" Number of atoms: 11510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1452, 11510 Classifications: {'peptide': 1452} Link IDs: {'PCIS': 2, 'PTRANS': 68, 'TRANS': 1381} Chain breaks: 1 Chain: "p" Number of atoms: 9149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1146, 9149 Classifications: {'peptide': 1146} Link IDs: {'PTRANS': 53, 'TRANS': 1092} Chain breaks: 1 Chain: "q" 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: "r" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1050 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "s" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "t" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "u" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "v" 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: "w" 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: "x" 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: "y" 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: "z" 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: "Z" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'W0F': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "w" 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: "x" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "z" 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 4709 SG CYS o 71 114.084 112.528 115.101 1.00141.57 S ATOM 4731 SG CYS o 74 111.807 115.440 115.215 1.00137.29 S ATOM 4778 SG CYS o 81 110.391 111.841 114.997 1.00138.71 S ATOM 5013 SG CYS o 111 101.691 111.241 68.337 1.00164.45 S ATOM 5041 SG CYS o 114 103.771 114.633 68.034 1.00163.67 S ATOM 5387 SG CYS o 184 103.785 111.997 65.243 1.00171.81 S ATOM 24474 SG CYS p1119 105.507 124.979 104.004 1.00141.59 S ATOM 24496 SG CYS p1122 105.458 121.777 101.851 1.00142.57 S ATOM 24611 SG CYS p1137 108.325 122.461 103.994 1.00148.67 S ATOM 24632 SG CYS p1140 107.812 124.321 100.753 1.00152.98 S ATOM 25598 SG CYS q 88 85.446 90.728 173.510 1.00138.12 S ATOM 25611 SG CYS q 90 88.897 89.862 172.320 1.00147.15 S ATOM 25646 SG CYS q 94 87.125 87.472 174.632 1.00132.97 S ATOM 25668 SG CYS q 97 85.727 87.800 171.203 1.00132.45 S ATOM 32974 SG CYS w 17 75.543 52.500 55.844 1.00161.53 S ATOM 32998 SG CYS w 20 78.933 53.577 57.374 1.00163.91 S ATOM 33159 SG CYS w 39 76.809 56.290 56.410 1.00169.29 S ATOM 33184 SG CYS w 42 78.072 53.991 53.684 1.00167.79 S ATOM 33536 SG CYS w 86 44.325 43.182 86.150 1.00150.39 S ATOM 33560 SG CYS w 89 44.911 39.705 87.842 1.00155.57 S ATOM 33764 SG CYS w 114 46.645 42.843 89.119 1.00146.35 S ATOM 33799 SG CYS w 119 47.447 41.341 85.663 1.00152.45 S ATOM 33909 SG CYS x 7 65.616 72.329 151.601 1.00 98.61 S ATOM 33933 SG CYS x 10 63.948 73.354 154.825 1.00 95.35 S ATOM 34197 SG CYS x 44 61.770 72.499 151.635 1.00107.46 S ATOM 34203 SG CYS x 45 63.275 70.130 154.051 1.00108.23 S ATOM 35349 SG CYS z 19 107.203 61.353 142.299 1.00146.64 S ATOM 35368 SG CYS z 22 107.999 58.787 144.862 1.00145.85 S ATOM 35485 SG CYS z 36 110.768 61.258 143.920 1.00153.01 S ATOM 35511 SG CYS z 39 109.449 58.883 141.257 1.00150.68 S Time building chain proxies: 18.35, per 1000 atoms: 0.51 Number of scatterers: 35721 At special positions: 0 Unit cell: (165.416, 185.426, 192.096, 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 8 29.99 S 203 16.00 P 113 15.00 Mg 1 11.99 O 6951 8.00 N 6272 7.00 C 22150 6.00 H 23 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.44 Conformation dependent library (CDL) restraints added in 6.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN o2001 " pdb="ZN ZN o2001 " - pdb=" NE2 HIS o 84 " pdb="ZN ZN o2001 " - pdb=" SG CYS o 71 " pdb="ZN ZN o2001 " - pdb=" SG CYS o 74 " pdb="ZN ZN o2001 " - pdb=" SG CYS o 81 " pdb=" ZN o2002 " pdb="ZN ZN o2002 " - pdb=" SG CYS o 184 " pdb="ZN ZN o2002 " - pdb=" SG CYS o 111 " pdb="ZN ZN o2002 " - pdb=" SG CYS o 114 " pdb=" ZN p1201 " pdb="ZN ZN p1201 " - pdb=" SG CYS p1137 " pdb="ZN ZN p1201 " - pdb=" SG CYS p1122 " pdb="ZN ZN p1201 " - pdb=" SG CYS p1140 " pdb="ZN ZN p1201 " - pdb=" SG CYS p1119 " pdb=" ZN q 301 " pdb="ZN ZN q 301 " - pdb=" SG CYS q 94 " pdb="ZN ZN q 301 " - pdb=" SG CYS q 88 " pdb="ZN ZN q 301 " - pdb=" SG CYS q 90 " pdb="ZN ZN q 301 " - pdb=" SG CYS q 97 " pdb=" ZN w 201 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 42 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 20 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 17 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 39 " pdb=" ZN w 202 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 119 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 114 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 89 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 86 " pdb=" ZN x 101 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 10 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 45 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 44 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 7 " pdb=" ZN z 101 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 39 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 19 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 22 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 36 " Number of angles added : 39 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7864 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 139 helices and 44 sheets defined 32.3% alpha, 15.0% beta 43 base pairs and 93 stacking pairs defined. Time for finding SS restraints: 15.24 Creating SS restraints... Processing helix chain 'S' and resid 6 through 8 No H-bonds generated for 'chain 'S' and resid 6 through 8' Processing helix chain 'S' and resid 33 through 35 No H-bonds generated for 'chain 'S' and resid 33 through 35' Processing helix chain 'S' and resid 157 through 165 Processing helix chain 'S' and resid 173 through 179 Processing helix chain 'T' and resid 10 through 14 Processing helix chain 'T' and resid 25 through 34 removed outlier: 4.170A pdb=" N ALA T 34 " --> pdb=" O GLN T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 63 No H-bonds generated for 'chain 'T' and resid 60 through 63' Processing helix chain 'o' and resid 28 through 34 Processing helix chain 'o' and resid 99 through 109 Processing helix chain 'o' and resid 124 through 132 Processing helix chain 'o' and resid 137 through 150 removed outlier: 4.270A pdb=" N GLY o 150 " --> pdb=" O ASP o 146 " (cutoff:3.500A) Processing helix chain 'o' and resid 218 through 227 removed outlier: 3.879A pdb=" N ARG o 227 " --> pdb=" O GLU o 223 " (cutoff:3.500A) Processing helix chain 'o' and resid 230 through 236 Processing helix chain 'o' and resid 245 through 248 No H-bonds generated for 'chain 'o' and resid 245 through 248' Processing helix chain 'o' and resid 275 through 296 Processing helix chain 'o' and resid 302 through 318 Processing helix chain 'o' and resid 339 through 343 Processing helix chain 'o' and resid 349 through 352 No H-bonds generated for 'chain 'o' and resid 349 through 352' Processing helix chain 'o' and resid 382 through 387 Processing helix chain 'o' and resid 399 through 408 Processing helix chain 'o' and resid 435 through 438 removed outlier: 3.610A pdb=" N LEU o 438 " --> pdb=" O PRO o 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 435 through 438' Processing helix chain 'o' and resid 466 through 468 No H-bonds generated for 'chain 'o' and resid 466 through 468' Processing helix chain 'o' and resid 486 through 492 removed outlier: 4.095A pdb=" N THR o 490 " --> pdb=" O SER o 487 " (cutoff:3.500A) Proline residue: o 491 - end of helix Processing helix chain 'o' and resid 509 through 519 Processing helix chain 'o' and resid 521 through 524 Processing helix chain 'o' and resid 539 through 548 removed outlier: 3.561A pdb=" N LYS o 547 " --> pdb=" O ALA o 544 " (cutoff:3.500A) Processing helix chain 'o' and resid 557 through 566 removed outlier: 3.806A pdb=" N PHE o 566 " --> pdb=" O ASN o 562 " (cutoff:3.500A) Processing helix chain 'o' and resid 588 through 595 removed outlier: 3.865A pdb=" N LEU o 594 " --> pdb=" O GLN o 590 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE o 595 " --> pdb=" O ILE o 591 " (cutoff:3.500A) Processing helix chain 'o' and resid 611 through 615 removed outlier: 4.205A pdb=" N SER o 615 " --> pdb=" O ASP o 611 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 611 through 615' Processing helix chain 'o' and resid 642 through 645 No H-bonds generated for 'chain 'o' and resid 642 through 645' Processing helix chain 'o' and resid 652 through 660 Processing helix chain 'o' and resid 662 through 683 Processing helix chain 'o' and resid 689 through 692 No H-bonds generated for 'chain 'o' and resid 689 through 692' Processing helix chain 'o' and resid 696 through 721 Processing helix chain 'o' and resid 733 through 759 Processing helix chain 'o' and resid 765 through 772 Processing helix chain 'o' and resid 778 through 785 Processing helix chain 'o' and resid 817 through 820 No H-bonds generated for 'chain 'o' and resid 817 through 820' Processing helix chain 'o' and resid 833 through 867 removed outlier: 4.420A pdb=" N ALA o 855 " --> pdb=" O ALA o 851 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU o 856 " --> pdb=" O VAL o 852 " (cutoff:3.500A) Processing helix chain 'o' and resid 891 through 893 No H-bonds generated for 'chain 'o' and resid 891 through 893' Processing helix chain 'o' and resid 913 through 920 Processing helix chain 'o' and resid 927 through 933 Processing helix chain 'o' and resid 936 through 944 Processing helix chain 'o' and resid 946 through 969 Processing helix chain 'o' and resid 983 through 993 Processing helix chain 'o' and resid 1006 through 1018 Processing helix chain 'o' and resid 1028 through 1037 Processing helix chain 'o' and resid 1039 through 1048 Processing helix chain 'o' and resid 1051 through 1056 Processing helix chain 'o' and resid 1062 through 1079 Processing helix chain 'o' and resid 1087 through 1101 Proline residue: o1098 - end of helix removed outlier: 4.122A pdb=" N GLN o1101 " --> pdb=" O GLU o1097 " (cutoff:3.500A) Processing helix chain 'o' and resid 1121 through 1129 Processing helix chain 'o' and resid 1151 through 1161 Processing helix chain 'o' and resid 1166 through 1169 No H-bonds generated for 'chain 'o' and resid 1166 through 1169' Processing helix chain 'o' and resid 1188 through 1198 removed outlier: 3.746A pdb=" N GLU o1191 " --> pdb=" O GLU o1188 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL o1193 " --> pdb=" O GLN o1190 " (cutoff:3.500A) Processing helix chain 'o' and resid 1218 through 1223 Processing helix chain 'o' and resid 1228 through 1239 Processing helix chain 'o' and resid 1263 through 1267 Processing helix chain 'o' and resid 1282 through 1295 Processing helix chain 'o' and resid 1343 through 1348 Processing helix chain 'o' and resid 1362 through 1369 Processing helix chain 'o' and resid 1371 through 1387 Processing helix chain 'o' and resid 1395 through 1406 Processing helix chain 'o' and resid 1416 through 1419 No H-bonds generated for 'chain 'o' and resid 1416 through 1419' Processing helix chain 'o' and resid 1426 through 1431 Processing helix chain 'o' and resid 1435 through 1445 removed outlier: 3.840A pdb=" N MET o1440 " --> pdb=" O ASP o1437 " (cutoff:3.500A) Processing helix chain 'o' and resid 1454 through 1459 Processing helix chain 'o' and resid 1477 through 1481 Processing helix chain 'p' and resid 22 through 36 removed outlier: 3.816A pdb=" N TRP p 27 " --> pdb=" O GLN p 23 " (cutoff:3.500A) Processing helix chain 'p' and resid 41 through 61 Processing helix chain 'p' and resid 110 through 115 Processing helix chain 'p' and resid 168 through 173 Processing helix chain 'p' and resid 247 through 252 Processing helix chain 'p' and resid 269 through 275 Processing helix chain 'p' and resid 281 through 288 Processing helix chain 'p' and resid 295 through 307 Proline residue: p 303 - end of helix Processing helix chain 'p' and resid 314 through 323 Processing helix chain 'p' and resid 332 through 345 Processing helix chain 'p' and resid 358 through 377 Processing helix chain 'p' and resid 388 through 390 No H-bonds generated for 'chain 'p' and resid 388 through 390' Processing helix chain 'p' and resid 396 through 425 Processing helix chain 'p' and resid 431 through 434 No H-bonds generated for 'chain 'p' and resid 431 through 434' Processing helix chain 'p' and resid 437 through 450 Processing helix chain 'p' and resid 475 through 482 Processing helix chain 'p' and resid 503 through 505 No H-bonds generated for 'chain 'p' and resid 503 through 505' Processing helix chain 'p' and resid 539 through 548 Processing helix chain 'p' and resid 580 through 593 Processing helix chain 'p' and resid 637 through 644 Processing helix chain 'p' and resid 653 through 658 Processing helix chain 'p' and resid 667 through 672 removed outlier: 3.782A pdb=" N THR p 672 " --> pdb=" O LEU p 668 " (cutoff:3.500A) Processing helix chain 'p' and resid 679 through 682 No H-bonds generated for 'chain 'p' and resid 679 through 682' Processing helix chain 'p' and resid 700 through 703 Processing helix chain 'p' and resid 714 through 716 No H-bonds generated for 'chain 'p' and resid 714 through 716' Processing helix chain 'p' and resid 719 through 731 removed outlier: 3.760A pdb=" N GLN p 731 " --> pdb=" O ALA p 727 " (cutoff:3.500A) Processing helix chain 'p' and resid 762 through 767 Processing helix chain 'p' and resid 798 through 803 Processing helix chain 'p' and resid 969 through 975 Proline residue: p 973 - end of helix Processing helix chain 'p' and resid 978 through 993 Processing helix chain 'p' and resid 1008 through 1018 removed outlier: 3.555A pdb=" N ASP p1017 " --> pdb=" O ASN p1013 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR p1018 " --> pdb=" O LEU p1014 " (cutoff:3.500A) Processing helix chain 'p' and resid 1055 through 1058 No H-bonds generated for 'chain 'p' and resid 1055 through 1058' Processing helix chain 'p' and resid 1088 through 1097 Processing helix chain 'p' and resid 1100 through 1111 removed outlier: 4.117A pdb=" N ALA p1110 " --> pdb=" O ARG p1106 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER p1111 " --> pdb=" O LEU p1107 " (cutoff:3.500A) Processing helix chain 'p' and resid 1153 through 1164 Processing helix chain 'q' and resid 28 through 40 Processing helix chain 'q' and resid 61 through 70 Processing helix chain 'q' and resid 78 through 81 No H-bonds generated for 'chain 'q' and resid 78 through 81' Processing helix chain 'q' and resid 117 through 119 No H-bonds generated for 'chain 'q' and resid 117 through 119' Processing helix chain 'q' and resid 174 through 176 No H-bonds generated for 'chain 'q' and resid 174 through 176' Processing helix chain 'q' and resid 200 through 202 No H-bonds generated for 'chain 'q' and resid 200 through 202' Processing helix chain 'q' and resid 241 through 270 removed outlier: 3.562A pdb=" N VAL q 245 " --> pdb=" O PRO q 241 " (cutoff:3.500A) Processing helix chain 'r' and resid 24 through 27 No H-bonds generated for 'chain 'r' and resid 24 through 27' Processing helix chain 'r' and resid 34 through 50 Processing helix chain 'r' and resid 59 through 70 Processing helix chain 'r' and resid 77 through 89 Processing helix chain 'r' and resid 94 through 103 Processing helix chain 'r' and resid 108 through 114 Processing helix chain 'r' and resid 116 through 118 No H-bonds generated for 'chain 'r' and resid 116 through 118' Processing helix chain 'r' and resid 124 through 137 Processing helix chain 's' and resid 3 through 23 Processing helix chain 's' and resid 30 through 33 No H-bonds generated for 'chain 's' and resid 30 through 33' Processing helix chain 's' and resid 37 through 44 Processing helix chain 's' and resid 84 through 97 Processing helix chain 's' and resid 112 through 120 Processing helix chain 's' and resid 132 through 136 Processing helix chain 's' and resid 139 through 141 No H-bonds generated for 'chain 's' and resid 139 through 141' Processing helix chain 's' and resid 153 through 162 Processing helix chain 's' and resid 178 through 183 Processing helix chain 't' and resid 59 through 75 Processing helix chain 't' and resid 89 through 99 Processing helix chain 'u' and resid 15 through 17 No H-bonds generated for 'chain 'u' and resid 15 through 17' Processing helix chain 'u' and resid 22 through 34 Processing helix chain 'w' and resid 70 through 74 Processing helix chain 'x' and resid 18 through 27 Processing helix chain 'x' and resid 31 through 38 Processing helix chain 'x' and resid 43 through 50 removed outlier: 3.606A pdb=" N MET x 48 " --> pdb=" O CYS x 44 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU x 49 " --> pdb=" O CYS x 45 " (cutoff:3.500A) Processing helix chain 'x' and resid 56 through 61 removed outlier: 3.688A pdb=" N ASN x 61 " --> pdb=" O GLU x 57 " (cutoff:3.500A) Processing helix chain 'y' and resid 6 through 9 Processing helix chain 'y' and resid 40 through 52 removed outlier: 3.828A pdb=" N ILE y 45 " --> pdb=" O THR y 41 " (cutoff:3.500A) Processing helix chain 'y' and resid 83 through 112 Processing sheet with id= A, first strand: chain 'S' and resid 27 through 31 removed outlier: 6.827A pdb=" N ASN S 142 " --> pdb=" O ILE S 28 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ALA S 30 " --> pdb=" O ASN S 142 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TYR S 144 " --> pdb=" O ALA S 30 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE S 113 " --> pdb=" O ASN S 145 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS S 109 " --> pdb=" O LEU S 149 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'S' and resid 125 through 128 removed outlier: 3.581A pdb=" N ILE S 126 " --> pdb=" O PHE S 138 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE S 138 " --> pdb=" O ILE S 126 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR S 128 " --> pdb=" O GLU S 136 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU S 136 " --> pdb=" O THR S 128 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'T' and resid 41 through 47 removed outlier: 11.281A pdb=" N THR T 52 " --> pdb=" O LEU T 85 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LEU T 85 " --> pdb=" O THR T 52 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL T 54 " --> pdb=" O PHE T 83 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG T 113 " --> pdb=" O GLN T 86 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N LEU T 20 " --> pdb=" O VAL T 111 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG T 113 " --> pdb=" O LEU T 20 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LYS T 22 " --> pdb=" O ARG T 113 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLU T 115 " --> pdb=" O LYS T 22 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'T' and resid 94 through 98 removed outlier: 3.602A pdb=" N GLY T 108 " --> pdb=" O VAL T 95 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR T 97 " --> pdb=" O LEU T 106 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N LEU T 106 " --> pdb=" O THR T 97 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'o' and resid 86 through 89 Processing sheet with id= F, first strand: chain 'o' and resid 190 through 194 removed outlier: 4.618A pdb=" N LEU o 198 " --> pdb=" O LEU o 216 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'o' and resid 264 through 266 Processing sheet with id= H, first strand: chain 'o' and resid 362 through 366 removed outlier: 3.549A pdb=" N THR o 365 " --> pdb=" O MET o 501 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'o' and resid 367 through 369 removed outlier: 6.103A pdb=" N PHE o 482 " --> pdb=" O THR o 368 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'o' and resid 389 through 393 removed outlier: 3.896A pdb=" N TYR o 418 " --> pdb=" O GLU o 447 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N HIS o 449 " --> pdb=" O ALA o 416 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ALA o 416 " --> pdb=" O HIS o 449 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'o' and resid 602 through 604 removed outlier: 3.576A pdb=" N MET o 637 " --> pdb=" O VAL o 629 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU o 631 " --> pdb=" O LEU o 635 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LEU o 635 " --> pdb=" O GLU o 631 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'o' and resid 902 through 905 Processing sheet with id= M, first strand: chain 'o' and resid 1138 through 1142 removed outlier: 3.659A pdb=" N LYS o1306 " --> pdb=" O ASP o1339 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'o' and resid 1244 through 1247 removed outlier: 4.353A pdb=" N LEU o1255 " --> pdb=" O LEU o1216 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA o1174 " --> pdb=" O ARG o1213 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'o' and resid 1319 through 1322 Processing sheet with id= P, first strand: chain 'p' and resid 65 through 67 Processing sheet with id= Q, first strand: chain 'p' and resid 91 through 93 removed outlier: 3.744A pdb=" N GLY p 150 " --> pdb=" O LEU p 124 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL p 126 " --> pdb=" O PHE p 148 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N PHE p 148 " --> pdb=" O VAL p 126 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'p' and resid 97 through 99 Processing sheet with id= S, first strand: chain 'p' and resid 185 through 187 Processing sheet with id= T, first strand: chain 'p' and resid 197 through 200 Processing sheet with id= U, first strand: chain 'p' and resid 205 through 208 removed outlier: 6.873A pdb=" N MET p 239 " --> pdb=" O ALA p 216 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N THR p 218 " --> pdb=" O VAL p 237 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL p 237 " --> pdb=" O THR p 218 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU p 220 " --> pdb=" O ILE p 235 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE p 235 " --> pdb=" O GLU p 220 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ARG p 222 " --> pdb=" O SER p 233 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N SER p 233 " --> pdb=" O ARG p 222 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP p 236 " --> pdb=" O THR p 259 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'p' and resid 484 through 486 Processing sheet with id= W, first strand: chain 'p' and resid 530 through 532 Processing sheet with id= X, first strand: chain 'p' and resid 748 through 751 removed outlier: 3.535A pdb=" N GLN p 906 " --> pdb=" O ARG p 922 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ARG p 924 " --> pdb=" O VAL p 904 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL p 904 " --> pdb=" O ARG p 924 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'p' and resid 945 through 949 removed outlier: 6.907A pdb=" N VAL p 794 " --> pdb=" O GLY p 946 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLN p 948 " --> pdb=" O VAL p 794 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N MET p 796 " --> pdb=" O GLN p 948 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE p1042 " --> pdb=" O ILE p 782 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'p' and resid 827 through 829 Processing sheet with id= AA, first strand: chain 'p' and resid 1113 through 1119 Processing sheet with id= AB, first strand: chain 'p' and resid 1127 through 1129 Processing sheet with id= AC, first strand: chain 'q' and resid 182 through 185 removed outlier: 6.809A pdb=" N ILE q 22 " --> pdb=" O ILE q 11 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE q 11 " --> pdb=" O ILE q 22 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU q 24 " --> pdb=" O VAL q 9 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N VAL q 9 " --> pdb=" O GLU q 24 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'q' and resid 98 through 106 removed outlier: 6.081A pdb=" N LYS q 166 " --> pdb=" O ILE q 47 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE q 47 " --> pdb=" O LYS q 166 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLY q 168 " --> pdb=" O ILE q 45 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE q 45 " --> pdb=" O GLY q 168 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'q' and resid 113 through 116 Processing sheet with id= AF, first strand: chain 's' and resid 60 through 62 removed outlier: 6.265A pdb=" N ILE s 126 " --> pdb=" O ALA s 102 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE s 104 " --> pdb=" O ILE s 126 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU s 128 " --> pdb=" O ILE s 104 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL s 106 " --> pdb=" O GLU s 128 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N PHE s 130 " --> pdb=" O VAL s 106 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 's' and resid 147 through 150 removed outlier: 3.648A pdb=" N GLU s 147 " --> pdb=" O ILE s 194 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 't' and resid 105 through 109 Processing sheet with id= AI, first strand: chain 'u' and resid 2 through 13 Processing sheet with id= AJ, first strand: chain 'u' and resid 142 through 146 removed outlier: 7.009A pdb=" N PHE u 98 " --> pdb=" O THR u 90 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N VAL u 92 " --> pdb=" O GLY u 96 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N GLY u 96 " --> pdb=" O VAL u 92 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER u 105 " --> pdb=" O ILE u 157 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N SER u 109 " --> pdb=" O GLY u 161 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY u 149 " --> pdb=" O ILE u 160 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N SER u 162 " --> pdb=" O ILE u 147 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE u 147 " --> pdb=" O SER u 162 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'u' and resid 127 through 129 Processing sheet with id= AL, first strand: chain 'u' and resid 44 through 48 removed outlier: 6.852A pdb=" N ILE u 75 " --> pdb=" O ILE u 46 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'u' and resid 50 through 54 removed outlier: 6.844A pdb=" N LYS u 71 " --> pdb=" O ASP u 52 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'v' and resid 25 through 31 removed outlier: 5.247A pdb=" N LEU v 122 " --> pdb=" O ASP v 42 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER v 117 " --> pdb=" O VAL v 96 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N VAL v 96 " --> pdb=" O SER v 117 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LYS v 55 " --> pdb=" O LEU v 148 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N HIS v 29 " --> pdb=" O LYS v 13 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'w' and resid 24 through 28 Processing sheet with id= AP, first strand: chain 'w' and resid 79 through 81 Processing sheet with id= AQ, first strand: chain 'y' and resid 19 through 23 Processing sheet with id= AR, first strand: chain 'z' and resid 16 through 18 1151 hydrogen bonds defined for protein. 3237 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 108 hydrogen bonds 216 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 93 stacking parallelities Total time for adding SS restraints: 17.66 Time building geometry restraints manager: 16.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.17: 23 1.17 - 1.33: 9014 1.33 - 1.49: 12403 1.49 - 1.65: 14855 1.65 - 1.81: 325 Bond restraints: 36620 Sorted by residual: bond pdb=" C4' G2L Z 11 " pdb=" C3' G2L Z 11 " ideal model delta sigma weight residual 1.270 1.524 -0.254 2.00e-02 2.50e+03 1.62e+02 bond pdb=" C2' G2L Z 11 " pdb=" C1' G2L Z 11 " ideal model delta sigma weight residual 1.271 1.480 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" P G2L Z 11 " pdb=" O5' G2L Z 11 " ideal model delta sigma weight residual 1.685 1.496 0.189 2.00e-02 2.50e+03 8.94e+01 bond pdb=" C4' G2L Z 11 " pdb=" O4' G2L Z 11 " ideal model delta sigma weight residual 1.560 1.394 0.166 2.00e-02 2.50e+03 6.88e+01 bond pdb=" N GLY N 3 " pdb=" H GLY N 3 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 ... (remaining 36615 not shown) Histogram of bond angle deviations from ideal: 75.41 - 88.77: 3 88.77 - 102.13: 285 102.13 - 115.49: 24080 115.49 - 128.85: 25286 128.85 - 142.21: 309 Bond angle restraints: 49963 Sorted by residual: angle pdb=" O3' A Z 10 " pdb=" P G2L Z 11 " pdb=" O5' G2L Z 11 " ideal model delta sigma weight residual 104.00 76.36 27.64 1.50e+00 4.44e-01 3.40e+02 angle pdb=" N09 W0F Z2500 " pdb=" C06 W0F Z2500 " pdb=" O05 W0F Z2500 " ideal model delta sigma weight residual 110.18 75.41 34.77 3.00e+00 1.11e-01 1.34e+02 angle pdb=" C07 W0F Z2500 " pdb=" C06 W0F Z2500 " pdb=" N09 W0F Z2500 " ideal model delta sigma weight residual 110.46 136.30 -25.84 3.00e+00 1.11e-01 7.42e+01 angle pdb=" C5' G2L Z 11 " pdb=" C4' G2L Z 11 " pdb=" O4' G2L Z 11 " ideal model delta sigma weight residual 110.08 87.22 22.86 3.00e+00 1.11e-01 5.81e+01 angle pdb=" P26 W0F Z2500 " pdb=" O29 W0F Z2500 " pdb=" P30 W0F Z2500 " ideal model delta sigma weight residual 123.60 142.21 -18.61 3.00e+00 1.11e-01 3.85e+01 ... (remaining 49958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 21369 35.97 - 71.93: 717 71.93 - 107.90: 31 107.90 - 143.86: 0 143.86 - 179.83: 1 Dihedral angle restraints: 22118 sinusoidal: 9958 harmonic: 12160 Sorted by residual: dihedral pdb=" CA TRP o 479 " pdb=" C TRP o 479 " pdb=" N SER o 480 " pdb=" CA SER o 480 " ideal model delta harmonic sigma weight residual -180.00 -154.47 -25.53 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA LEU o 343 " pdb=" C LEU o 343 " pdb=" N LYS o 344 " pdb=" CA LYS o 344 " ideal model delta harmonic sigma weight residual -180.00 -159.15 -20.85 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA VAL o1341 " pdb=" C VAL o1341 " pdb=" N SER o1342 " pdb=" CA SER o1342 " ideal model delta harmonic sigma weight residual 180.00 160.15 19.85 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 22115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4868 0.074 - 0.148: 667 0.148 - 0.223: 15 0.223 - 0.297: 4 0.297 - 0.371: 3 Chirality restraints: 5557 Sorted by residual: chirality pdb=" C06 W0F Z2500 " pdb=" C07 W0F Z2500 " pdb=" N09 W0F Z2500 " pdb=" O05 W0F Z2500 " both_signs ideal model delta sigma weight residual False 2.41 2.04 0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CA HYP N 8 " pdb=" N HYP N 8 " pdb=" C HYP N 8 " pdb=" CB HYP N 8 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" C03 W0F Z2500 " pdb=" C04 W0F Z2500 " pdb=" C07 W0F Z2500 " pdb=" O02 W0F Z2500 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.62e+00 ... (remaining 5554 not shown) Planarity restraints: 6101 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 W0F Z2500 " -0.108 2.00e-02 2.50e+03 4.13e-02 5.12e+01 pdb=" C10 W0F Z2500 " 0.040 2.00e-02 2.50e+03 pdb=" C12 W0F Z2500 " 0.007 2.00e-02 2.50e+03 pdb=" C13 W0F Z2500 " 0.031 2.00e-02 2.50e+03 pdb=" C15 W0F Z2500 " 0.008 2.00e-02 2.50e+03 pdb=" C17 W0F Z2500 " -0.020 2.00e-02 2.50e+03 pdb=" N09 W0F Z2500 " 0.052 2.00e-02 2.50e+03 pdb=" N11 W0F Z2500 " 0.013 2.00e-02 2.50e+03 pdb=" N14 W0F Z2500 " 0.031 2.00e-02 2.50e+03 pdb=" N16 W0F Z2500 " -0.017 2.00e-02 2.50e+03 pdb=" N19 W0F Z2500 " 0.006 2.00e-02 2.50e+03 pdb=" O18 W0F Z2500 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE p 51 " -0.022 2.00e-02 2.50e+03 4.53e-02 2.05e+01 pdb=" C ILE p 51 " 0.078 2.00e-02 2.50e+03 pdb=" O ILE p 51 " -0.030 2.00e-02 2.50e+03 pdb=" N GLN p 52 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE p 50 " -0.020 2.00e-02 2.50e+03 4.03e-02 1.62e+01 pdb=" C PHE p 50 " 0.070 2.00e-02 2.50e+03 pdb=" O PHE p 50 " -0.026 2.00e-02 2.50e+03 pdb=" N ILE p 51 " -0.024 2.00e-02 2.50e+03 ... (remaining 6098 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.40: 46 2.40 - 2.95: 16263 2.95 - 3.50: 41251 3.50 - 4.05: 70531 4.05 - 4.60: 102001 Nonbonded interactions: 230092 Sorted by model distance: nonbonded pdb=" OD1 ASP o 495 " pdb="MG MG o2003 " model vdw 1.850 2.050 nonbonded pdb=" C10 W0F Z2500 " pdb=" O05 W0F Z2500 " model vdw 1.871 2.520 nonbonded pdb=" OD1 ASP o 497 " pdb="MG MG o2003 " model vdw 1.922 2.050 nonbonded pdb="HG22 ILE N 4 " pdb="HD13 ILE N 4 " model vdw 2.018 2.440 nonbonded pdb=" OD2 ASP o 497 " pdb=" O33 W0F Z2500 " model vdw 2.035 2.800 ... (remaining 230087 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.860 Extract box with map and model: 8.620 Check model and map are aligned: 0.490 Set scattering table: 0.310 Process input model: 108.600 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.120 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:14.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5224 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.254 36597 Z= 0.503 Angle : 0.807 34.769 49911 Z= 0.411 Chirality : 0.048 0.371 5557 Planarity : 0.005 0.058 6097 Dihedral : 15.338 179.829 14249 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.92 % Favored : 95.91 % Rotamer: Outliers : 1.38 % Allowed : 5.99 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 4137 helix: 1.22 (0.14), residues: 1416 sheet: 0.21 (0.20), residues: 685 loop : -0.27 (0.13), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP o1192 HIS 0.008 0.001 HIS o 809 PHE 0.020 0.002 PHE q 93 TYR 0.031 0.002 TYR o 669 ARG 0.008 0.001 ARG p 483 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1007 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 956 time to evaluate : 4.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 8 residues processed: 987 average time/residue: 1.7237 time to fit residues: 2006.0164 Evaluate side-chains 555 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 547 time to evaluate : 3.899 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 5.4151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 355 optimal weight: 0.9990 chunk 319 optimal weight: 0.0070 chunk 177 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 215 optimal weight: 3.9990 chunk 170 optimal weight: 0.7980 chunk 329 optimal weight: 50.0000 chunk 127 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 chunk 245 optimal weight: 0.6980 chunk 382 optimal weight: 2.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 178 GLN o 181 HIS ** o 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 531 ASN ** o 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 671 ASN o 704 ASN o 721 HIS o 731 ASN o 780 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 792 ASN ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 904 GLN o 945 ASN o1044 HIS ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1230 GLN o1310 HIS o1410 HIS o1462 GLN p 43 GLN p 56 GLN p 98 HIS p 144 HIS p 145 GLN p 164 ASN p 245 GLN ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 525 ASN p 537 GLN p 577 HIS p 639 HIS p 650 ASN p 699 HIS p 838 GLN p 941 GLN p1007 ASN p1021 HIS p1068 GLN p1115 GLN p1133 HIS ** p1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 18 ASN ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 232 ASN r 66 ASN r 129 GLN s 64 HIS s 138 ASN t 46 GLN u 14 HIS u 24 ASN u 28 GLN v 44 ASN v 76 ASN w 22 ASN w 45 GLN w 50 ASN w 74 GLN ** w 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 98 GLN ** y 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5265 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 36597 Z= 0.181 Angle : 0.491 9.220 49911 Z= 0.265 Chirality : 0.040 0.166 5557 Planarity : 0.003 0.054 6097 Dihedral : 16.545 176.870 5795 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 24.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.53 % Favored : 96.30 % Rotamer: Outliers : 3.71 % Allowed : 16.54 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.84 (0.13), residues: 4137 helix: 1.80 (0.14), residues: 1401 sheet: 0.28 (0.20), residues: 675 loop : -0.15 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP o1192 HIS 0.007 0.001 HIS r 43 PHE 0.016 0.001 PHE o 234 TYR 0.012 0.001 TYR p 388 ARG 0.007 0.000 ARG p 975 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 578 time to evaluate : 4.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 137 outliers final: 57 residues processed: 652 average time/residue: 1.6653 time to fit residues: 1295.6907 Evaluate side-chains 561 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 504 time to evaluate : 3.804 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 38 residues processed: 21 average time/residue: 0.5630 time to fit residues: 23.6046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 212 optimal weight: 0.1980 chunk 118 optimal weight: 2.9990 chunk 318 optimal weight: 0.9980 chunk 260 optimal weight: 0.0770 chunk 105 optimal weight: 4.9990 chunk 383 optimal weight: 0.7980 chunk 413 optimal weight: 2.9990 chunk 341 optimal weight: 2.9990 chunk 379 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 307 optimal weight: 4.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 62 GLN o 372 ASN ** o 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 904 GLN o1044 HIS o1093 GLN ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1410 HIS ** o1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 117 ASN p 254 GLN p 265 GLN ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 650 ASN p 718 GLN p1007 ASN ** p1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p1133 HIS ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 28 GLN v 76 ASN w 22 ASN w 45 GLN w 74 GLN ** w 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 98 GLN ** y 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5285 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36597 Z= 0.170 Angle : 0.459 11.124 49911 Z= 0.247 Chirality : 0.039 0.181 5557 Planarity : 0.003 0.049 6097 Dihedral : 16.093 177.292 5795 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 26.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.94 % Favored : 95.89 % Rotamer: Outliers : 4.47 % Allowed : 17.19 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.10 (0.13), residues: 4137 helix: 2.08 (0.14), residues: 1404 sheet: 0.32 (0.19), residues: 687 loop : -0.00 (0.14), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP o1192 HIS 0.015 0.001 HIS r 43 PHE 0.018 0.001 PHE p 309 TYR 0.028 0.001 TYR u 3 ARG 0.007 0.000 ARG o1149 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 539 time to evaluate : 3.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 165 outliers final: 72 residues processed: 635 average time/residue: 1.6017 time to fit residues: 1219.9081 Evaluate side-chains 564 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 492 time to evaluate : 4.265 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 49 residues processed: 25 average time/residue: 0.7465 time to fit residues: 32.5502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 378 optimal weight: 0.0980 chunk 287 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 chunk 384 optimal weight: 2.9990 chunk 406 optimal weight: 0.7980 chunk 200 optimal weight: 5.9990 chunk 364 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 22 GLN o 372 ASN ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 671 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o1032 GLN o1163 HIS o1410 HIS ** o1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 56 GLN p 111 ASN ** p 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 500 GLN p 650 ASN p 749 HIS p 980 HIS ** p1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p1115 GLN p1133 HIS ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 28 GLN v 76 ASN w 22 ASN w 45 GLN w 74 GLN ** w 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 98 GLN ** y 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5346 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 36597 Z= 0.365 Angle : 0.542 10.068 49911 Z= 0.288 Chirality : 0.043 0.186 5557 Planarity : 0.004 0.052 6097 Dihedral : 16.091 178.859 5795 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 26.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.38 % Favored : 95.48 % Rotamer: Outliers : 4.80 % Allowed : 17.90 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.76 (0.13), residues: 4137 helix: 1.72 (0.14), residues: 1417 sheet: 0.13 (0.19), residues: 666 loop : -0.17 (0.14), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP t 118 HIS 0.014 0.001 HIS r 43 PHE 0.021 0.002 PHE o 113 TYR 0.015 0.002 TYR p 92 ARG 0.008 0.001 ARG p 938 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 529 time to evaluate : 4.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 177 outliers final: 97 residues processed: 639 average time/residue: 1.6642 time to fit residues: 1268.8316 Evaluate side-chains 593 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 496 time to evaluate : 4.005 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 63 residues processed: 36 average time/residue: 0.8429 time to fit residues: 48.2258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 338 optimal weight: 1.9990 chunk 231 optimal weight: 0.9990 chunk 5 optimal weight: 50.0000 chunk 302 optimal weight: 0.7980 chunk 167 optimal weight: 0.8980 chunk 347 optimal weight: 0.1980 chunk 281 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 365 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 485 ASN ** o 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 671 ASN o 673 GLN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o1146 GLN o1410 HIS ** o1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 145 GLN p 500 GLN p 518 HIS p 650 ASN p 718 GLN p1115 GLN p1133 HIS ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 28 GLN v 76 ASN v 131 ASN w 22 ASN w 45 GLN ** w 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 36 ASN ** y 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5324 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36597 Z= 0.185 Angle : 0.450 9.931 49911 Z= 0.241 Chirality : 0.039 0.163 5557 Planarity : 0.003 0.044 6097 Dihedral : 15.941 177.982 5795 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 28.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.23 % Favored : 95.62 % Rotamer: Outliers : 4.12 % Allowed : 19.20 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.97 (0.13), residues: 4137 helix: 2.02 (0.14), residues: 1410 sheet: 0.23 (0.19), residues: 666 loop : -0.13 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP o 679 HIS 0.014 0.001 HIS r 43 PHE 0.020 0.001 PHE y 13 TYR 0.012 0.001 TYR p 388 ARG 0.005 0.000 ARG p 770 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 523 time to evaluate : 4.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 152 outliers final: 91 residues processed: 620 average time/residue: 1.6777 time to fit residues: 1247.7520 Evaluate side-chains 592 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 501 time to evaluate : 4.021 Switching outliers to nearest non-outliers outliers start: 91 outliers final: 64 residues processed: 29 average time/residue: 0.7242 time to fit residues: 35.7526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 136 optimal weight: 0.0370 chunk 366 optimal weight: 20.0000 chunk 80 optimal weight: 0.8980 chunk 238 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 407 optimal weight: 2.9990 chunk 338 optimal weight: 3.9990 chunk 188 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 213 optimal weight: 0.7980 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 353 ASN ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 459 ASN ** o 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o1146 GLN ** o1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1410 HIS ** o1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 500 GLN p 518 HIS p 525 ASN p 650 ASN p1133 HIS ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 28 GLN w 91 HIS ** y 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5338 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 36597 Z= 0.236 Angle : 0.473 9.918 49911 Z= 0.252 Chirality : 0.040 0.163 5557 Planarity : 0.003 0.044 6097 Dihedral : 15.870 176.839 5795 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 27.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.57 % Favored : 95.29 % Rotamer: Outliers : 3.96 % Allowed : 19.96 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.95 (0.13), residues: 4137 helix: 2.02 (0.14), residues: 1408 sheet: 0.25 (0.19), residues: 663 loop : -0.17 (0.14), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP o 679 HIS 0.012 0.001 HIS r 43 PHE 0.019 0.001 PHE y 13 TYR 0.012 0.001 TYR t 115 ARG 0.007 0.000 ARG o 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 505 time to evaluate : 4.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 146 outliers final: 100 residues processed: 596 average time/residue: 1.5788 time to fit residues: 1125.8904 Evaluate side-chains 589 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 489 time to evaluate : 4.065 Switching outliers to nearest non-outliers outliers start: 100 outliers final: 73 residues processed: 29 average time/residue: 0.5588 time to fit residues: 30.4372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 392 optimal weight: 8.9990 chunk 45 optimal weight: 0.3980 chunk 232 optimal weight: 2.9990 chunk 297 optimal weight: 0.5980 chunk 230 optimal weight: 0.5980 chunk 342 optimal weight: 0.6980 chunk 227 optimal weight: 3.9990 chunk 405 optimal weight: 1.9990 chunk 253 optimal weight: 0.9990 chunk 247 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1410 HIS ** o1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 56 GLN ** p 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 500 GLN p 518 HIS p 650 ASN p 718 GLN p1094 GLN ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5329 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36597 Z= 0.177 Angle : 0.440 9.781 49911 Z= 0.235 Chirality : 0.039 0.161 5557 Planarity : 0.003 0.041 6097 Dihedral : 15.745 175.880 5795 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 28.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.40 % Favored : 95.46 % Rotamer: Outliers : 3.39 % Allowed : 20.72 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.09 (0.13), residues: 4137 helix: 2.19 (0.14), residues: 1408 sheet: 0.35 (0.20), residues: 655 loop : -0.14 (0.14), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP o 679 HIS 0.011 0.001 HIS r 43 PHE 0.017 0.001 PHE y 13 TYR 0.014 0.001 TYR t 115 ARG 0.003 0.000 ARG v 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 504 time to evaluate : 4.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 125 outliers final: 87 residues processed: 596 average time/residue: 1.6091 time to fit residues: 1156.9487 Evaluate side-chains 583 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 496 time to evaluate : 4.242 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 71 residues processed: 18 average time/residue: 0.6152 time to fit residues: 22.7664 ------------------------------------------------------------------------------- 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: 58.334 > 50: distance: 27 - 32: 8.044 distance: 32 - 33: 4.813 distance: 32 - 208: 8.449 distance: 33 - 34: 7.421 distance: 34 - 35: 4.935 distance: 34 - 40: 4.410 distance: 35 - 205: 10.283 distance: 36 - 37: 13.413 distance: 36 - 38: 8.300 distance: 37 - 39: 8.602 distance: 40 - 41: 12.116 distance: 41 - 44: 7.447 distance: 42 - 43: 40.670 distance: 42 - 48: 20.632 distance: 44 - 45: 20.183 distance: 45 - 46: 6.299 distance: 46 - 47: 13.571 distance: 48 - 49: 6.719 distance: 49 - 50: 33.795 distance: 49 - 52: 19.052 distance: 50 - 51: 32.623 distance: 50 - 56: 12.489 distance: 52 - 53: 12.362 distance: 53 - 54: 33.422 distance: 53 - 55: 10.732 distance: 56 - 57: 9.483 distance: 57 - 58: 18.166 distance: 57 - 60: 24.947 distance: 58 - 59: 14.454 distance: 58 - 67: 13.946 distance: 59 - 85: 23.267 distance: 60 - 61: 20.001 distance: 61 - 62: 25.995 distance: 62 - 63: 5.940 distance: 63 - 64: 24.190 distance: 64 - 65: 3.900 distance: 64 - 66: 4.399 distance: 67 - 68: 3.783 distance: 68 - 69: 10.848 distance: 68 - 71: 12.494 distance: 69 - 70: 4.903 distance: 69 - 73: 5.488 distance: 70 - 93: 12.808 distance: 71 - 72: 6.988 distance: 73 - 74: 10.077 distance: 74 - 75: 6.261 distance: 74 - 77: 14.765 distance: 75 - 76: 5.278 distance: 75 - 78: 3.842 distance: 78 - 79: 7.038 distance: 79 - 80: 3.286 distance: 79 - 82: 7.748 distance: 80 - 81: 10.241 distance: 80 - 85: 8.316 distance: 82 - 83: 10.424 distance: 82 - 84: 13.276 distance: 85 - 86: 4.263 distance: 86 - 87: 3.268 distance: 86 - 89: 15.563 distance: 87 - 88: 4.414 distance: 87 - 93: 7.713 distance: 89 - 90: 6.628 distance: 90 - 91: 14.915 distance: 93 - 94: 4.821 distance: 94 - 95: 8.239 distance: 94 - 97: 10.596 distance: 95 - 96: 5.503 distance: 95 - 104: 8.291 distance: 97 - 98: 14.821 distance: 98 - 99: 9.854 distance: 99 - 100: 4.228 distance: 100 - 101: 7.792 distance: 101 - 102: 9.429 distance: 101 - 103: 6.309 distance: 104 - 105: 4.458 distance: 105 - 106: 9.955 distance: 106 - 107: 8.210 distance: 106 - 108: 3.250