Starting phenix.real_space_refine (version: 1.21rc1) on Sat Jul 15 20:55:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7u_13245/07_2023/7p7u_13245_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7u_13245/07_2023/7p7u_13245.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7u_13245/07_2023/7p7u_13245_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7u_13245/07_2023/7p7u_13245_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7u_13245/07_2023/7p7u_13245_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7u_13245/07_2023/7p7u_13245.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7u_13245/07_2023/7p7u_13245.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7u_13245/07_2023/7p7u_13245_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7u_13245/07_2023/7p7u_13245_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.002 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 152 8.98 5 Zn 4 6.06 5 P 4549 5.49 5 Mg 186 5.21 5 S 134 5.16 5 C 69804 2.51 5 N 25814 2.21 5 O 39183 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "d TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 139826 Number of models: 1 Model: "" Number of chains: 64 Chain: "1" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 491 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "2" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 428 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "3" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 647 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "4" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 406 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "5" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 410 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "6" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 374 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "7" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 522 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "8" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 305 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 33} Chain: "A" Number of atoms: 60606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2824, 60606 Classifications: {'RNA': 2824} Modifications used: {'rna2p_pur': 288, 'rna2p_pyr': 147, 'rna3p_pur': 1350, 'rna3p_pyr': 1039} Link IDs: {'rna2p': 434, 'rna3p': 2389} Chain breaks: 3 Chain: "B" Number of atoms: 2439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 2439 Classifications: {'RNA': 114} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 56, 'rna3p_pyr': 45} Link IDs: {'rna2p': 12, 'rna3p': 101} Chain: "D" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1644 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 34, 'rna3p_pyr': 33} Link IDs: {'rna2p': 10, 'rna3p': 66} Chain: "G" Number of atoms: 2106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2106 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 16, 'TRANS': 257} Chain: "H" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1572 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "I" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1572 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 8, 'TRANS': 196} Chain: "J" Number of atoms: 1392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1392 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Chain: "K" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1335 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 9, 'TRANS': 164} Chain: "M" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1146 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 7, 'TRANS': 139} Chain: "N" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 923 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "O" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1096 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain: "P" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1070 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 6, 'TRANS': 127} Chain: "Q" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 997 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "R" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 908 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "S" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 925 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "T" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 950 Classifications: {'peptide': 118} Link IDs: {'TRANS': 117} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 779 Classifications: {'peptide': 101} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 97} Chain: "V" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 841 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "W" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 736 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "X" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 763 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "Y" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 559 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "Z" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 480 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "a" Number of atoms: 32595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1521, 32595 Classifications: {'RNA': 1521} Modifications used: {'rna2p_pur': 112, 'rna2p_pyr': 87, 'rna3p_pur': 741, 'rna3p_pyr': 581} Link IDs: {'rna2p': 199, 'rna3p': 1321} Chain breaks: 2 Chain: "b" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 285 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 10} Chain breaks: 1 Chain: "c" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1773 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 8, 'TRANS': 213} Chain: "d" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1618 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain: "e" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1611 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 8, 'TRANS': 191} Chain: "f" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1204 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "g" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 786 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "h" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1218 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "i" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "j" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 980 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "k" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 773 Classifications: {'peptide': 96} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 89} Chain: "l" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 854 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain: "m" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1051 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 8, 'TRANS': 125} Chain: "n" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 902 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "o" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "p" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 716 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "q" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 692 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "r" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 660 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "s" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 511 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "t" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 663 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "u" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 608 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 241 Unusual residues: {' K': 103, ' MG': 138} Classifications: {'undetermined': 241} Link IDs: {None: 240} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 3, ' MG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 3, ' MG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 111 Unusual residues: {' K': 38, ' MG': 44, 'PUT': 1, 'SCM': 1} Classifications: {'undetermined': 84} Link IDs: {None: 83} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1794 SG CYS 4 30 70.258 63.580 134.408 1.00123.62 S ATOM 1814 SG CYS 4 33 70.910 60.512 132.218 1.00132.25 S ATOM 1892 SG CYS 4 43 71.925 63.993 131.039 1.00125.85 S ATOM 1910 SG CYS 4 46 68.261 63.037 131.253 1.00126.81 S ATOM 2044 SG CYS 5 9 201.898 111.163 77.273 1.00104.48 S ATOM 2063 SG CYS 5 12 200.729 108.235 75.632 1.00112.82 S ATOM 2276 SG CYS 5 36 201.516 108.166 78.993 1.00108.98 S ATOM 3363 SG CYS 8 11 142.953 143.040 170.836 1.00119.51 S ATOM 3388 SG CYS 8 14 142.369 139.575 169.208 1.00106.67 S ATOM 3494 SG CYS 8 27 139.730 141.135 171.546 1.00111.86 S ATOM A0R8E SG CYS o 24 164.158 228.760 108.778 1.00114.25 S ATOM A0R94 SG CYS o 27 161.539 226.193 109.769 1.00119.38 S ATOM A0RC8 SG CYS o 40 163.126 225.963 106.352 1.00119.33 S ATOM A0RCX SG CYS o 43 160.712 228.716 107.082 1.00112.81 S Time building chain proxies: 46.00, per 1000 atoms: 0.33 Number of scatterers: 139826 At special positions: 0 Unit cell: (254.2, 278.8, 218.12, 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 4 29.99 K 152 19.00 S 134 16.00 P 4549 15.00 Mg 186 11.99 O 39183 8.00 N 25814 7.00 C 69804 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 61.83 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 46 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 30 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 43 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 33 " pdb=" ZN 5 101 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 12 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 36 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 9 " pdb=" ZN 8 101 " pdb="ZN ZN 8 101 " - pdb=" ND1 HIS 8 33 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 11 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 27 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 14 " pdb=" ZN o 102 " pdb="ZN ZN o 102 " - pdb=" SG CYS o 27 " pdb="ZN ZN o 102 " - pdb=" SG CYS o 43 " pdb="ZN ZN o 102 " - pdb=" SG CYS o 40 " pdb="ZN ZN o 102 " - pdb=" SG CYS o 24 " Number of angles added : 15 10490 Ramachandran restraints generated. 5245 Oldfield, 0 Emsley, 5245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9794 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 164 helices and 76 sheets defined 38.2% alpha, 20.0% beta 1587 base pairs and 2263 stacking pairs defined. Time for finding SS restraints: 64.27 Creating SS restraints... Processing helix chain '1' and resid 2 through 10 removed outlier: 4.952A pdb=" N THR 1 10 " --> pdb=" O ILE 1 6 " (cutoff:3.500A) Processing helix chain '1' and resid 11 through 35 removed outlier: 3.988A pdb=" N GLY 1 35 " --> pdb=" O GLN 1 31 " (cutoff:3.500A) Processing helix chain '1' and resid 39 through 60 removed outlier: 4.447A pdb=" N ILE 1 43 " --> pdb=" O ASN 1 39 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS 1 44 " --> pdb=" O THR 1 40 " (cutoff:3.500A) Processing helix chain '2' and resid 16 through 27 Processing helix chain '2' and resid 40 through 51 Processing helix chain '3' and resid 55 through 60 Processing helix chain '3' and resid 69 through 79 Processing helix chain '4' and resid 9 through 21 removed outlier: 4.687A pdb=" N HIS 4 19 " --> pdb=" O LYS 4 15 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N TYR 4 20 " --> pdb=" O ARG 4 16 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LYS 4 21 " --> pdb=" O ARG 4 17 " (cutoff:3.500A) Processing helix chain '5' and resid 22 through 27 Proline residue: 5 27 - end of helix Processing helix chain '6' and resid 8 through 16 Processing helix chain '6' and resid 17 through 25 removed outlier: 3.994A pdb=" N THR 6 24 " --> pdb=" O LYS 6 20 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LYS 6 25 " --> pdb=" O ARG 6 21 " (cutoff:3.500A) Processing helix chain '6' and resid 26 through 38 Processing helix chain '7' and resid 7 through 14 Processing helix chain '7' and resid 32 through 37 removed outlier: 4.322A pdb=" N LYS 7 36 " --> pdb=" O ARG 7 32 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N THR 7 37 " --> pdb=" O PHE 7 33 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 32 through 37' Processing helix chain '7' and resid 38 through 46 removed outlier: 4.000A pdb=" N LYS 7 46 " --> pdb=" O ARG 7 42 " (cutoff:3.500A) Processing helix chain '7' and resid 51 through 63 removed outlier: 5.716A pdb=" N GLN 7 60 " --> pdb=" O LYS 7 56 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N GLN 7 61 " --> pdb=" O ARG 7 57 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU 7 62 " --> pdb=" O ILE 7 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 136 removed outlier: 3.641A pdb=" N ILE G 135 " --> pdb=" O PRO G 131 " (cutoff:3.500A) Proline residue: G 136 - end of helix No H-bonds generated for 'chain 'G' and resid 131 through 136' Processing helix chain 'G' and resid 207 through 215 removed outlier: 3.644A pdb=" N SER G 211 " --> pdb=" O LYS G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 226 removed outlier: 3.946A pdb=" N MET G 225 " --> pdb=" O ARG G 221 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASN G 226 " --> pdb=" O GLY G 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 221 through 226' Processing helix chain 'G' and resid 264 through 271 removed outlier: 4.843A pdb=" N LYS G 268 " --> pdb=" O ALA G 264 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU G 269 " --> pdb=" O LYS G 265 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VAL G 271 " --> pdb=" O ASP G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 202 removed outlier: 4.288A pdb=" N GLU G 201 " --> pdb=" O GLU G 198 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 62 removed outlier: 4.762A pdb=" N ASN H 62 " --> pdb=" O GLU H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 71 removed outlier: 4.189A pdb=" N LYS H 71 " --> pdb=" O GLY H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 92 removed outlier: 3.811A pdb=" N TYR H 91 " --> pdb=" O GLU H 87 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLU H 92 " --> pdb=" O LEU H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 92' Processing helix chain 'H' and resid 98 through 103 removed outlier: 4.796A pdb=" N PHE H 102 " --> pdb=" O LYS H 98 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N GLN H 103 " --> pdb=" O VAL H 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 98 through 103' Processing helix chain 'H' and resid 121 through 126 Processing helix chain 'H' and resid 40 through 45 Processing helix chain 'I' and resid 29 through 46 removed outlier: 3.686A pdb=" N ARG I 45 " --> pdb=" O ARG I 41 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N GLN I 46 " --> pdb=" O ALA I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 58 removed outlier: 5.855A pdb=" N ARG I 58 " --> pdb=" O ARG I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 121 Processing helix chain 'I' and resid 135 through 147 Processing helix chain 'I' and resid 160 through 169 removed outlier: 4.388A pdb=" N ASN I 169 " --> pdb=" O LEU I 165 " (cutoff:3.500A) Processing helix chain 'I' and resid 182 through 190 removed outlier: 5.155A pdb=" N ASN I 190 " --> pdb=" O VAL I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 206 Processing helix chain 'J' and resid 2 through 21 removed outlier: 3.577A pdb=" N VAL J 12 " --> pdb=" O TYR J 8 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR J 13 " --> pdb=" O ILE J 9 " (cutoff:3.500A) Proline residue: J 14 - end of helix Processing helix chain 'J' and resid 41 through 46 removed outlier: 4.656A pdb=" N SER J 45 " --> pdb=" O GLY J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 62 Processing helix chain 'J' and resid 93 through 111 removed outlier: 3.666A pdb=" N SER J 107 " --> pdb=" O LEU J 103 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU J 108 " --> pdb=" O VAL J 104 " (cutoff:3.500A) Proline residue: J 109 - end of helix Processing helix chain 'J' and resid 162 through 174 Processing helix chain 'J' and resid 134 through 139 removed outlier: 4.507A pdb=" N ILE J 137 " --> pdb=" O GLU J 134 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N PHE J 138 " --> pdb=" O GLN J 135 " (cutoff:3.500A) Proline residue: J 139 - end of helix No H-bonds generated for 'chain 'J' and resid 134 through 139' Processing helix chain 'K' and resid 3 through 8 removed outlier: 5.265A pdb=" N VAL K 8 " --> pdb=" O ILE K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 81 Processing helix chain 'K' and resid 137 through 153 removed outlier: 4.115A pdb=" N ARG K 152 " --> pdb=" O ILE K 148 " (cutoff:3.500A) Proline residue: K 153 - end of helix Processing helix chain 'M' and resid 25 through 39 Processing helix chain 'M' and resid 89 through 97 Processing helix chain 'M' and resid 98 through 111 removed outlier: 3.502A pdb=" N MET M 109 " --> pdb=" O SER M 105 " (cutoff:3.500A) Proline residue: M 111 - end of helix Processing helix chain 'M' and resid 113 through 123 removed outlier: 3.767A pdb=" N LYS M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU M 123 " --> pdb=" O GLN M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 68 through 73 removed outlier: 4.190A pdb=" N LYS M 73 " --> pdb=" O LYS M 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 68 through 73' Processing helix chain 'N' and resid 104 through 110 removed outlier: 4.458A pdb=" N GLU N 108 " --> pdb=" O ARG N 104 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 118 Processing helix chain 'O' and resid 56 through 62 Proline residue: O 62 - end of helix Processing helix chain 'O' and resid 78 through 85 removed outlier: 4.223A pdb=" N ARG O 84 " --> pdb=" O ASP O 80 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N PHE O 85 " --> pdb=" O THR O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 100 Processing helix chain 'O' and resid 129 through 140 removed outlier: 3.506A pdb=" N GLY O 140 " --> pdb=" O ILE O 136 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 59 Processing helix chain 'P' and resid 110 through 126 Proline residue: P 126 - end of helix Processing helix chain 'Q' and resid 9 through 28 Processing helix chain 'Q' and resid 34 through 54 removed outlier: 4.468A pdb=" N SER Q 42 " --> pdb=" O LYS Q 38 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 66 removed outlier: 3.879A pdb=" N PHE Q 65 " --> pdb=" O GLN Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 84 through 98 removed outlier: 3.785A pdb=" N LEU Q 93 " --> pdb=" O LEU Q 89 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLY Q 94 " --> pdb=" O PHE Q 90 " (cutoff:3.500A) Proline residue: Q 95 - end of helix Processing helix chain 'R' and resid 6 through 22 removed outlier: 3.802A pdb=" N ARG R 17 " --> pdb=" O LYS R 13 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LYS R 21 " --> pdb=" O ARG R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 87 Processing helix chain 'R' and resid 102 through 115 Processing helix chain 'S' and resid 2 through 11 removed outlier: 4.349A pdb=" N GLU S 11 " --> pdb=" O GLU S 7 " (cutoff:3.500A) Processing helix chain 'S' and resid 97 through 104 removed outlier: 4.421A pdb=" N ARG S 101 " --> pdb=" O LEU S 97 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA S 102 " --> pdb=" O TYR S 98 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU S 103 " --> pdb=" O TYR S 99 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS S 104 " --> pdb=" O LEU S 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 97 through 104' Processing helix chain 'T' and resid 8 through 22 Processing helix chain 'T' and resid 25 through 31 removed outlier: 4.336A pdb=" N HIS T 29 " --> pdb=" O TYR T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 32 through 37 Processing helix chain 'T' and resid 39 through 73 removed outlier: 3.757A pdb=" N ARG T 51 " --> pdb=" O PHE T 47 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS T 54 " --> pdb=" O ARG T 50 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG T 55 " --> pdb=" O ARG T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 75 through 87 Processing helix chain 'T' and resid 91 through 101 Processing helix chain 'T' and resid 102 through 119 Processing helix chain 'V' and resid 18 through 30 removed outlier: 3.980A pdb=" N LEU V 28 " --> pdb=" O LEU V 24 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE V 29 " --> pdb=" O VAL V 25 " (cutoff:3.500A) Processing helix chain 'V' and resid 33 through 44 Processing helix chain 'V' and resid 46 through 66 removed outlier: 4.173A pdb=" N GLY V 50 " --> pdb=" O ASN V 46 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE V 51 " --> pdb=" O LYS V 47 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 8 removed outlier: 3.870A pdb=" N ILE W 7 " --> pdb=" O LEU W 3 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LYS W 8 " --> pdb=" O LEU W 4 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 23 Processing helix chain 'W' and resid 34 through 46 Processing helix chain 'X' and resid 64 through 69 removed outlier: 4.287A pdb=" N VAL X 68 " --> pdb=" O HIS X 64 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N MET X 69 " --> pdb=" O VAL X 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 64 through 69' Processing helix chain 'Z' and resid 50 through 57 removed outlier: 4.077A pdb=" N SER Z 56 " --> pdb=" O ARG Z 52 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLY Z 57 " --> pdb=" O ALA Z 53 " (cutoff:3.500A) Processing helix chain 'c' and resid 5 through 13 Processing helix chain 'c' and resid 24 through 32 removed outlier: 4.175A pdb=" N LYS c 28 " --> pdb=" O ASN c 24 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LYS c 29 " --> pdb=" O PRO c 25 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N TYR c 30 " --> pdb=" O LYS c 26 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N PHE c 32 " --> pdb=" O LYS c 28 " (cutoff:3.500A) Processing helix chain 'c' and resid 42 through 64 Processing helix chain 'c' and resid 74 through 88 removed outlier: 4.881A pdb=" N GLU c 78 " --> pdb=" O LYS c 74 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ALA c 79 " --> pdb=" O GLN c 75 " (cutoff:3.500A) Processing helix chain 'c' and resid 103 through 124 removed outlier: 3.655A pdb=" N GLU c 121 " --> pdb=" O ILE c 117 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU c 122 " --> pdb=" O ASN c 118 " (cutoff:3.500A) Processing helix chain 'c' and resid 125 through 130 Proline residue: c 130 - end of helix Processing helix chain 'c' and resid 131 through 148 Processing helix chain 'c' and resid 165 through 170 Processing helix chain 'c' and resid 171 through 180 Processing helix chain 'c' and resid 192 through 197 removed outlier: 4.458A pdb=" N ILE c 196 " --> pdb=" O ASP c 192 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASP c 197 " --> pdb=" O PRO c 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 192 through 197' Processing helix chain 'c' and resid 206 through 225 Processing helix chain 'd' and resid 6 through 12 Processing helix chain 'd' and resid 27 through 47 Processing helix chain 'd' and resid 71 through 77 Processing helix chain 'd' and resid 80 through 95 Processing helix chain 'd' and resid 107 through 112 removed outlier: 4.118A pdb=" N ASP d 111 " --> pdb=" O LYS d 107 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ALA d 112 " --> pdb=" O PRO d 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 107 through 112' Processing helix chain 'd' and resid 113 through 126 Processing helix chain 'd' and resid 128 through 144 Processing helix chain 'e' and resid 7 through 16 removed outlier: 4.380A pdb=" N VAL e 11 " --> pdb=" O PRO e 7 " (cutoff:3.500A) Processing helix chain 'e' and resid 23 through 28 removed outlier: 4.928A pdb=" N ARG e 28 " --> pdb=" O LYS e 24 " (cutoff:3.500A) Processing helix chain 'e' and resid 45 through 62 Processing helix chain 'e' and resid 64 through 78 removed outlier: 3.570A pdb=" N ILE e 78 " --> pdb=" O LYS e 74 " (cutoff:3.500A) Processing helix chain 'e' and resid 82 through 94 Processing helix chain 'e' and resid 95 through 103 Processing helix chain 'e' and resid 107 through 118 Processing helix chain 'e' and resid 143 through 148 removed outlier: 4.732A pdb=" N ASN e 148 " --> pdb=" O GLU e 144 " (cutoff:3.500A) Processing helix chain 'e' and resid 149 through 159 Processing helix chain 'e' and resid 182 through 187 removed outlier: 4.574A pdb=" N TYR e 187 " --> pdb=" O ARG e 183 " (cutoff:3.500A) Processing helix chain 'e' and resid 191 through 201 removed outlier: 3.517A pdb=" N VAL e 195 " --> pdb=" O ASP e 191 " (cutoff:3.500A) Processing helix chain 'e' and resid 34 through 39 Proline residue: e 38 - end of helix Processing helix chain 'f' and resid 55 through 71 Processing helix chain 'f' and resid 109 through 119 removed outlier: 3.697A pdb=" N ALA f 113 " --> pdb=" O GLY f 109 " (cutoff:3.500A) Processing helix chain 'f' and resid 132 through 148 removed outlier: 5.460A pdb=" N LYS f 148 " --> pdb=" O LEU f 144 " (cutoff:3.500A) Processing helix chain 'f' and resid 149 through 158 Processing helix chain 'f' and resid 160 through 165 Processing helix chain 'g' and resid 18 through 37 removed outlier: 3.764A pdb=" N GLY g 37 " --> pdb=" O LEU g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 75 through 87 Processing helix chain 'h' and resid 20 through 31 Processing helix chain 'h' and resid 35 through 54 Processing helix chain 'h' and resid 57 through 70 Processing helix chain 'h' and resid 92 through 111 Processing helix chain 'h' and resid 115 through 130 Processing helix chain 'h' and resid 132 through 149 Processing helix chain 'i' and resid 5 through 21 Processing helix chain 'i' and resid 30 through 44 Processing helix chain 'i' and resid 114 through 122 Processing helix chain 'j' and resid 34 through 40 Proline residue: j 40 - end of helix Processing helix chain 'j' and resid 41 through 56 Proline residue: j 51 - end of helix Processing helix chain 'j' and resid 71 through 92 Proline residue: j 92 - end of helix Processing helix chain 'j' and resid 93 through 102 removed outlier: 4.725A pdb=" N ALA j 97 " --> pdb=" O ASP j 93 " (cutoff:3.500A) Processing helix chain 'k' and resid 14 through 33 Processing helix chain 'k' and resid 80 through 91 removed outlier: 4.234A pdb=" N VAL k 84 " --> pdb=" O THR k 80 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP k 85 " --> pdb=" O PRO k 81 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N MET k 88 " --> pdb=" O VAL k 84 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ASP k 91 " --> pdb=" O LEU k 87 " (cutoff:3.500A) Processing helix chain 'l' and resid 46 through 51 removed outlier: 3.510A pdb=" N GLY l 51 " --> pdb=" O ALA l 47 " (cutoff:3.500A) Processing helix chain 'l' and resid 54 through 60 removed outlier: 4.233A pdb=" N SER l 58 " --> pdb=" O GLY l 54 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR l 59 " --> pdb=" O SER l 55 " (cutoff:3.500A) Proline residue: l 60 - end of helix No H-bonds generated for 'chain 'l' and resid 54 through 60' Processing helix chain 'l' and resid 61 through 78 Processing helix chain 'l' and resid 92 through 104 Processing helix chain 'm' and resid 3 through 11 Proline residue: m 11 - end of helix Processing helix chain 'm' and resid 21 through 27 removed outlier: 4.108A pdb=" N ASN m 25 " --> pdb=" O SER m 21 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS m 26 " --> pdb=" O PRO m 22 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N GLY m 27 " --> pdb=" O ALA m 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 21 through 27' Processing helix chain 'm' and resid 126 through 131 removed outlier: 4.444A pdb=" N TYR m 130 " --> pdb=" O SER m 126 " (cutoff:3.500A) Processing helix chain 'n' and resid 14 through 22 removed outlier: 3.701A pdb=" N TYR n 21 " --> pdb=" O VAL n 17 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE n 22 " --> pdb=" O SER n 18 " (cutoff:3.500A) Processing helix chain 'n' and resid 26 through 38 Processing helix chain 'n' and resid 44 through 49 removed outlier: 3.611A pdb=" N LEU n 48 " --> pdb=" O ARG n 44 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N THR n 49 " --> pdb=" O VAL n 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 44 through 49' Processing helix chain 'n' and resid 50 through 64 removed outlier: 3.593A pdb=" N LEU n 63 " --> pdb=" O GLU n 59 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LYS n 64 " --> pdb=" O ILE n 60 " (cutoff:3.500A) Processing helix chain 'n' and resid 66 through 84 Processing helix chain 'n' and resid 85 through 94 Processing helix chain 'n' and resid 106 through 111 Processing helix chain 'o' and resid 2 through 13 Proline residue: o 13 - end of helix Processing helix chain 'o' and resid 40 through 51 Processing helix chain 'p' and resid 4 through 16 Processing helix chain 'p' and resid 24 through 47 Processing helix chain 'p' and resid 49 through 74 removed outlier: 3.540A pdb=" N GLY p 55 " --> pdb=" O HIS p 51 " (cutoff:3.500A) Processing helix chain 'p' and resid 75 through 86 Processing helix chain 'q' and resid 52 through 63 Processing helix chain 'q' and resid 67 through 78 Processing helix chain 'q' and resid 79 through 88 Processing helix chain 's' and resid 15 through 21 Processing helix chain 's' and resid 29 through 38 removed outlier: 4.030A pdb=" N ARG s 35 " --> pdb=" O GLU s 31 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE s 36 " --> pdb=" O LEU s 32 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE s 37 " --> pdb=" O LEU s 33 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N SER s 38 " --> pdb=" O LYS s 34 " (cutoff:3.500A) Processing helix chain 's' and resid 45 through 50 Processing helix chain 's' and resid 52 through 70 Processing helix chain 't' and resid 12 through 24 removed outlier: 4.689A pdb=" N GLY t 24 " --> pdb=" O GLU t 20 " (cutoff:3.500A) Processing helix chain 't' and resid 70 through 76 removed outlier: 4.494A pdb=" N PHE t 74 " --> pdb=" O LYS t 70 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA t 75 " --> pdb=" O LEU t 71 " (cutoff:3.500A) Proline residue: t 76 - end of helix No H-bonds generated for 'chain 't' and resid 70 through 76' Processing helix chain 'u' and resid 4 through 42 Processing helix chain 'u' and resid 45 through 64 removed outlier: 4.233A pdb=" N LYS u 63 " --> pdb=" O MET u 59 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY u 64 " --> pdb=" O ALA u 60 " (cutoff:3.500A) Processing helix chain 'u' and resid 67 through 82 Processing sheet with id= 1, first strand: chain '2' and resid 32 through 38 removed outlier: 3.939A pdb=" N SER 2 33 " --> pdb=" O LEU 2 8 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU 2 53 " --> pdb=" O LYS 2 9 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '3' and resid 21 through 25 removed outlier: 3.841A pdb=" N PHE 3 21 " --> pdb=" O ASP 3 16 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLU 3 33 " --> pdb=" O LEU 3 45 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '4' and resid 27 through 30 removed outlier: 4.455A pdb=" N GLU 4 35 " --> pdb=" O CYS 4 30 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '5' and resid 3 through 8 Processing sheet with id= 5, first strand: chain '5' and resid 30 through 34 removed outlier: 5.690A pdb=" N LEU 5 30 " --> pdb=" O GLU 5 47 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '7' and resid 22 through 25 removed outlier: 5.758A pdb=" N LEU 7 22 " --> pdb=" O VAL 7 50 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '8' and resid 1 through 5 removed outlier: 6.108A pdb=" N HIS 8 33 " --> pdb=" O CYS 8 27 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N CYS 8 27 " --> pdb=" O HIS 8 33 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N VAL 8 23 " --> pdb=" O GLN 8 37 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'G' and resid 2 through 6 removed outlier: 6.375A pdb=" N ALA G 2 " --> pdb=" O ASP G 20 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N MET G 16 " --> pdb=" O TYR G 6 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'G' and resid 33 through 36 No H-bonds generated for sheet with id= 9 Processing sheet with id= 10, first strand: chain 'G' and resid 80 through 83 removed outlier: 6.502A pdb=" N LEU G 93 " --> pdb=" O LYS G 79 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N MET G 114 " --> pdb=" O VAL G 78 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N GLY G 127 " --> pdb=" O ARG G 115 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N VAL G 117 " --> pdb=" O GLY G 127 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'G' and resid 138 through 142 removed outlier: 4.102A pdb=" N THR G 139 " --> pdb=" O VAL G 164 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU G 180 " --> pdb=" O LEU G 176 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'G' and resid 91 through 96 removed outlier: 3.805A pdb=" N VAL G 100 " --> pdb=" O TYR G 96 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'H' and resid 3 through 8 removed outlier: 6.350A pdb=" N LYS H 3 " --> pdb=" O SER H 204 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N LEU H 199 " --> pdb=" O THR H 113 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR H 113 " --> pdb=" O LEU H 199 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASP H 167 " --> pdb=" O THR H 114 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'H' and resid 11 through 17 removed outlier: 3.866A pdb=" N GLU H 21 " --> pdb=" O THR H 17 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'H' and resid 33 through 36 removed outlier: 6.780A pdb=" N GLN H 50 " --> pdb=" O LEU H 36 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'H' and resid 106 through 109 removed outlier: 4.251A pdb=" N ASP H 106 " --> pdb=" O VAL H 176 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'I' and resid 2 through 7 removed outlier: 3.750A pdb=" N LEU I 6 " --> pdb=" O GLY I 15 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLY I 15 " --> pdb=" O LEU I 6 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'I' and resid 122 through 125 Processing sheet with id= 19, first strand: chain 'J' and resid 65 through 69 removed outlier: 4.263A pdb=" N GLY J 86 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE J 85 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N VAL J 40 " --> pdb=" O ILE J 85 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N GLY J 39 " --> pdb=" O GLY J 151 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLY J 151 " --> pdb=" O GLY J 39 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'K' and resid 16 through 19 Processing sheet with id= 21, first strand: chain 'K' and resid 41 through 45 Processing sheet with id= 22, first strand: chain 'K' and resid 94 through 99 removed outlier: 6.939A pdb=" N ASN K 101 " --> pdb=" O ALA K 117 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'K' and resid 121 through 125 removed outlier: 6.135A pdb=" N ILE K 132 " --> pdb=" O GLU K 124 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N THR K 129 " --> pdb=" O LEU K 89 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG K 163 " --> pdb=" O GLU K 88 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'M' and resid 53 through 58 removed outlier: 5.133A pdb=" N ASP M 20 " --> pdb=" O LEU M 141 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'M' and resid 75 through 79 removed outlier: 7.394A pdb=" N GLY M 84 " --> pdb=" O SER M 79 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'N' and resid 18 through 21 removed outlier: 4.645A pdb=" N SER N 6 " --> pdb=" O THR N 21 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ASN N 82 " --> pdb=" O ARG N 7 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'N' and resid 38 through 41 Processing sheet with id= 28, first strand: chain 'N' and resid 66 through 71 No H-bonds generated for sheet with id= 28 Processing sheet with id= 29, first strand: chain 'P' and resid 63 through 67 removed outlier: 7.155A pdb=" N MET P 103 " --> pdb=" O LYS P 67 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE P 104 " --> pdb=" O LEU P 34 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N GLU P 31 " --> pdb=" O ARG P 134 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LYS P 128 " --> pdb=" O THR P 37 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'P' and resid 72 through 75 Processing sheet with id= 31, first strand: chain 'Q' and resid 72 through 75 Processing sheet with id= 32, first strand: chain 'R' and resid 29 through 35 removed outlier: 3.823A pdb=" N ALA R 54 " --> pdb=" O VAL R 44 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'S' and resid 38 through 45 removed outlier: 6.632A pdb=" N THR S 25 " --> pdb=" O VAL S 87 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN S 83 " --> pdb=" O HIS S 29 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'S' and resid 49 through 52 removed outlier: 3.749A pdb=" N LYS S 49 " --> pdb=" O THR S 60 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'U' and resid 2 through 6 Processing sheet with id= 36, first strand: chain 'U' and resid 18 through 23 removed outlier: 4.306A pdb=" N GLN U 18 " --> pdb=" O ILE U 97 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LYS U 94 " --> pdb=" O GLU U 63 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLU U 59 " --> pdb=" O GLU U 98 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU U 31 " --> pdb=" O VAL U 62 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'U' and resid 39 through 42 removed outlier: 6.556A pdb=" N ILE U 39 " --> pdb=" O GLY U 49 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'U' and resid 64 through 67 Processing sheet with id= 39, first strand: chain 'U' and resid 70 through 76 Processing sheet with id= 40, first strand: chain 'V' and resid 6 through 13 removed outlier: 9.405A pdb=" N THR V 6 " --> pdb=" O GLU V 114 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL V 111 " --> pdb=" O SER V 77 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'V' and resid 78 through 84 removed outlier: 4.963A pdb=" N THR V 105 " --> pdb=" O GLY V 84 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'V' and resid 86 through 93 removed outlier: 4.241A pdb=" N SER V 97 " --> pdb=" O ARG V 93 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'W' and resid 24 through 29 removed outlier: 4.193A pdb=" N ARG W 76 " --> pdb=" O VAL W 29 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LYS W 73 " --> pdb=" O PRO W 60 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'X' and resid 9 through 12 removed outlier: 4.303A pdb=" N LYS X 19 " --> pdb=" O VAL X 11 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'X' and resid 25 through 28 removed outlier: 3.627A pdb=" N ALA X 25 " --> pdb=" O ILE X 34 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'X' and resid 39 through 45 removed outlier: 5.379A pdb=" N ASN X 39 " --> pdb=" O ALA X 61 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY X 55 " --> pdb=" O GLN X 45 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'X' and resid 80 through 83 removed outlier: 7.048A pdb=" N LYS X 80 " --> pdb=" O LYS X 95 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ARG X 92 " --> pdb=" O LEU X 101 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU X 99 " --> pdb=" O SER X 94 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'Y' and resid 46 through 49 removed outlier: 4.349A pdb=" N GLN Y 49 " --> pdb=" O ASP Y 66 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ASP Y 66 " --> pdb=" O GLN Y 49 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'Y' and resid 75 through 80 Processing sheet with id= 50, first strand: chain 'Z' and resid 12 through 19 No H-bonds generated for sheet with id= 50 Processing sheet with id= 51, first strand: chain 'c' and resid 15 through 18 removed outlier: 5.920A pdb=" N HIS c 15 " --> pdb=" O ILE c 41 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N TYR c 39 " --> pdb=" O GLY c 17 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'c' and resid 89 through 93 Processing sheet with id= 53, first strand: chain 'd' and resid 53 through 58 removed outlier: 3.682A pdb=" N THR d 53 " --> pdb=" O HIS d 68 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'd' and resid 163 through 168 removed outlier: 4.508A pdb=" N ASP d 180 " --> pdb=" O ARG d 203 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'e' and resid 166 through 170 Processing sheet with id= 56, first strand: chain 'f' and resid 11 through 16 removed outlier: 6.914A pdb=" N LEU f 36 " --> pdb=" O VAL f 16 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'f' and resid 83 through 88 removed outlier: 7.619A pdb=" N HIS f 83 " --> pdb=" O PRO f 98 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ARG f 93 " --> pdb=" O LEU f 128 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA f 99 " --> pdb=" O ASP f 122 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ASP f 122 " --> pdb=" O ALA f 99 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'f' and resid 32 through 41 removed outlier: 6.185A pdb=" N HIS f 45 " --> pdb=" O ASP f 41 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'g' and resid 38 through 41 removed outlier: 6.537A pdb=" N ASN g 67 " --> pdb=" O ILE g 41 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LYS g 6 " --> pdb=" O VAL g 98 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG g 92 " --> pdb=" O ILE g 12 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'g' and resid 42 through 45 Processing sheet with id= 61, first strand: chain 'g' and resid 46 through 50 Processing sheet with id= 62, first strand: chain 'h' and resid 72 through 79 removed outlier: 6.290A pdb=" N VAL h 72 " --> pdb=" O VAL h 91 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'i' and resid 23 through 28 removed outlier: 6.772A pdb=" N GLU i 23 " --> pdb=" O LEU i 64 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'i' and resid 76 through 79 removed outlier: 4.296A pdb=" N ASN i 76 " --> pdb=" O TRP i 132 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE i 105 " --> pdb=" O ILE i 128 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'j' and resid 5 through 11 Processing sheet with id= 66, first strand: chain 'k' and resid 35 through 38 removed outlier: 6.211A pdb=" N ARG k 7 " --> pdb=" O LYS k 101 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'k' and resid 39 through 42 removed outlier: 4.786A pdb=" N LYS k 71 " --> pdb=" O LEU k 42 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'k' and resid 44 through 52 Processing sheet with id= 69, first strand: chain 'l' and resid 42 through 45 removed outlier: 7.163A pdb=" N VAL l 84 " --> pdb=" O THR l 108 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'l' and resid 83 through 87 No H-bonds generated for sheet with id= 70 Processing sheet with id= 71, first strand: chain 'm' and resid 42 through 45 removed outlier: 5.141A pdb=" N LEU m 94 " --> pdb=" O VAL m 111 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'm' and resid 49 through 54 removed outlier: 5.355A pdb=" N LYS m 64 " --> pdb=" O ILE m 80 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'q' and resid 5 through 11 Processing sheet with id= 74, first strand: chain 'r' and resid 9 through 14 removed outlier: 5.399A pdb=" N LYS r 9 " --> pdb=" O GLU r 66 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LYS r 63 " --> pdb=" O LEU r 79 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'r' and resid 22 through 34 No H-bonds generated for sheet with id= 75 Processing sheet with id= 76, first strand: chain 't' and resid 30 through 34 removed outlier: 4.188A pdb=" N PHE t 47 " --> pdb=" O ILE t 62 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LYS t 56 " --> pdb=" O ASP t 53 " (cutoff:3.500A) 1825 hydrogen bonds defined for protein. 5367 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3958 hydrogen bonds 6198 hydrogen bond angles 0 basepair planarities 1587 basepair parallelities 2263 stacking parallelities Total time for adding SS restraints: 239.58 Time building geometry restraints manager: 66.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 13427 1.31 - 1.43: 67458 1.43 - 1.56: 61548 1.56 - 1.68: 9088 1.68 - 1.81: 248 Bond restraints: 151769 Sorted by residual: bond pdb=" C6 SCM a1660 " pdb=" O1 SCM a1660 " ideal model delta sigma weight residual 0.917 1.442 -0.525 2.00e-02 2.50e+03 6.89e+02 bond pdb=" C3 SCM a1660 " pdb=" C4 SCM a1660 " ideal model delta sigma weight residual 1.054 1.473 -0.419 2.00e-02 2.50e+03 4.39e+02 bond pdb=" C6 SCM a1660 " pdb=" O2B SCM a1660 " ideal model delta sigma weight residual 1.165 1.455 -0.290 2.00e-02 2.50e+03 2.10e+02 bond pdb=" C7 SCM a1660 " pdb=" O1B SCM a1660 " ideal model delta sigma weight residual 1.166 1.412 -0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C2 SCM a1660 " pdb=" C3 SCM a1660 " ideal model delta sigma weight residual 1.382 1.533 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 151764 not shown) Histogram of bond angle deviations from ideal: 100.04 - 106.84: 27834 106.84 - 113.63: 91160 113.63 - 120.43: 56782 120.43 - 127.23: 41642 127.23 - 134.02: 10033 Bond angle restraints: 227451 Sorted by residual: angle pdb=" C2' C a1390 " pdb=" C1' C a1390 " pdb=" N1 C a1390 " ideal model delta sigma weight residual 112.00 119.74 -7.74 1.50e+00 4.44e-01 2.66e+01 angle pdb=" O3' G A1061 " pdb=" C3' G A1061 " pdb=" C2' G A1061 " ideal model delta sigma weight residual 109.50 116.47 -6.97 1.50e+00 4.44e-01 2.16e+01 angle pdb=" C ALA K 13 " pdb=" CA ALA K 13 " pdb=" CB ALA K 13 " ideal model delta sigma weight residual 117.23 111.18 6.05 1.36e+00 5.41e-01 1.98e+01 angle pdb=" C4' G a 131 " pdb=" C3' G a 131 " pdb=" O3' G a 131 " ideal model delta sigma weight residual 109.40 115.25 -5.85 1.50e+00 4.44e-01 1.52e+01 angle pdb=" C3' A A 429 " pdb=" C2' A A 429 " pdb=" O2' A A 429 " ideal model delta sigma weight residual 114.60 108.83 5.77 1.50e+00 4.44e-01 1.48e+01 ... (remaining 227446 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 78429 35.87 - 71.73: 2270 71.73 - 107.60: 188 107.60 - 143.46: 31 143.46 - 179.33: 33 Dihedral angle restraints: 80951 sinusoidal: 65726 harmonic: 15225 Sorted by residual: dihedral pdb=" C4' A a 845 " pdb=" C3' A a 845 " pdb=" C2' A a 845 " pdb=" C1' A a 845 " ideal model delta sinusoidal sigma weight residual -35.00 33.74 -68.74 1 8.00e+00 1.56e-02 9.56e+01 dihedral pdb=" C4' G A1061 " pdb=" C3' G A1061 " pdb=" C2' G A1061 " pdb=" C1' G A1061 " ideal model delta sinusoidal sigma weight residual -35.00 32.17 -67.17 1 8.00e+00 1.56e-02 9.18e+01 dihedral pdb=" C4' A A 429 " pdb=" C3' A A 429 " pdb=" C2' A A 429 " pdb=" C1' A A 429 " ideal model delta sinusoidal sigma weight residual -35.00 31.50 -66.50 1 8.00e+00 1.56e-02 9.02e+01 ... (remaining 80948 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.967: 29147 0.967 - 1.935: 0 1.935 - 2.902: 0 2.902 - 3.869: 1 3.869 - 4.837: 1 Chirality restraints: 29149 Sorted by residual: chirality pdb=" C5 SCM a1660 " pdb=" C4 SCM a1660 " pdb=" C6 SCM a1660 " pdb=" O1B SCM a1660 " both_signs ideal model delta sigma weight residual False 2.40 -2.44 4.84 2.00e-01 2.50e+01 5.85e+02 chirality pdb=" C6 SCM a1660 " pdb=" C5 SCM a1660 " pdb=" O1 SCM a1660 " pdb=" O2B SCM a1660 " both_signs ideal model delta sigma weight residual False 1.09 -2.36 3.45 2.00e-01 2.50e+01 2.98e+02 chirality pdb=" C7 SCM a1660 " pdb=" C12 SCM a1660 " pdb=" C8 SCM a1660 " pdb=" O1B SCM a1660 " both_signs ideal model delta sigma weight residual False -1.93 -2.37 0.44 2.00e-01 2.50e+01 4.92e+00 ... (remaining 29146 not shown) Planarity restraints: 11892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 295 " -0.041 2.00e-02 2.50e+03 1.86e-02 1.03e+01 pdb=" N9 G A 295 " 0.046 2.00e-02 2.50e+03 pdb=" C8 G A 295 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G A 295 " -0.005 2.00e-02 2.50e+03 pdb=" C5 G A 295 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G A 295 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G A 295 " -0.013 2.00e-02 2.50e+03 pdb=" N1 G A 295 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G A 295 " -0.000 2.00e-02 2.50e+03 pdb=" N2 G A 295 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G A 295 " 0.007 2.00e-02 2.50e+03 pdb=" C4 G A 295 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A1019 " 0.039 2.00e-02 2.50e+03 1.78e-02 8.67e+00 pdb=" N9 A A1019 " -0.042 2.00e-02 2.50e+03 pdb=" C8 A A1019 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A A1019 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A A1019 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A A1019 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A A1019 " 0.010 2.00e-02 2.50e+03 pdb=" N1 A A1019 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A A1019 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A A1019 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A A1019 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A a 985 " 0.037 2.00e-02 2.50e+03 1.74e-02 8.32e+00 pdb=" N9 A a 985 " -0.043 2.00e-02 2.50e+03 pdb=" C8 A a 985 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A a 985 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A a 985 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A a 985 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A a 985 " 0.010 2.00e-02 2.50e+03 pdb=" N1 A a 985 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A a 985 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A a 985 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A a 985 " -0.001 2.00e-02 2.50e+03 ... (remaining 11889 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.41: 878 2.41 - 3.09: 98240 3.09 - 3.77: 330572 3.77 - 4.46: 495780 4.46 - 5.14: 656344 Nonbonded interactions: 1581814 Sorted by model distance: nonbonded pdb=" O2' G A 295 " pdb=" O5' G A 296 " model vdw 1.724 2.440 nonbonded pdb=" O3' G a1111 " pdb="MG MG a1681 " model vdw 1.789 2.170 nonbonded pdb=" O2' A A1413 " pdb=" O5' U A1414 " model vdw 1.797 2.440 nonbonded pdb=" OP2 A a1527 " pdb="MG MG a1627 " model vdw 1.801 2.170 nonbonded pdb=" OP2 C a1096 " pdb="MG MG a1679 " model vdw 1.816 2.170 ... (remaining 1581809 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: 4.030 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: 0.140 Extract box with map and model: 23.500 Check model and map are aligned: 1.550 Set scattering table: 0.900 Process input model: 529.030 Find NCS groups from input model: 2.600 Set up NCS constraints: 0.320 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: 0.030 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 564.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 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 0.525 151769 Z= 0.283 Angle : 0.519 10.733 227451 Z= 0.283 Chirality : 0.050 4.837 29149 Planarity : 0.004 0.096 11892 Dihedral : 13.967 179.331 71157 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.55 % Favored : 97.37 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 1.02 (0.12), residues: 5245 helix: 2.17 (0.12), residues: 1752 sheet: -0.10 (0.15), residues: 1062 loop : 0.00 (0.13), residues: 2431 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10490 Ramachandran restraints generated. 5245 Oldfield, 0 Emsley, 5245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10490 Ramachandran restraints generated. 5245 Oldfield, 0 Emsley, 5245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1015 residues out of total 4475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 996 time to evaluate : 5.973 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 6 residues processed: 1006 average time/residue: 1.2538 time to fit residues: 2160.4597 Evaluate side-chains 702 residues out of total 4475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 696 time to evaluate : 5.855 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 1.1113 time to fit residues: 17.9698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 817 optimal weight: 20.0000 chunk 733 optimal weight: 20.0000 chunk 407 optimal weight: 20.0000 chunk 250 optimal weight: 50.0000 chunk 494 optimal weight: 6.9990 chunk 391 optimal weight: 20.0000 chunk 758 optimal weight: 10.0000 chunk 293 optimal weight: 20.0000 chunk 461 optimal weight: 9.9990 chunk 564 optimal weight: 6.9990 chunk 879 optimal weight: 20.0000 overall best weight: 10.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 48 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 GLN H 62 ASN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 GLN c 8 GLN c 44 GLN ** c 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 133 GLN m 35 GLN t 57 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.063 151769 Z= 0.344 Angle : 0.592 26.017 227451 Z= 0.308 Chirality : 0.039 1.861 29149 Planarity : 0.004 0.060 11892 Dihedral : 13.973 179.708 60459 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.46 % Favored : 97.48 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 1.01 (0.12), residues: 5245 helix: 2.04 (0.12), residues: 1758 sheet: 0.05 (0.16), residues: 1036 loop : 0.03 (0.13), residues: 2451 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10490 Ramachandran restraints generated. 5245 Oldfield, 0 Emsley, 5245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10490 Ramachandran restraints generated. 5245 Oldfield, 0 Emsley, 5245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 4475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 730 time to evaluate : 6.049 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: 87 outliers final: 49 residues processed: 766 average time/residue: 1.3210 time to fit residues: 1765.0187 Evaluate side-chains 716 residues out of total 4475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 667 time to evaluate : 5.883 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 1.0919 time to fit residues: 106.5916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 488 optimal weight: 8.9990 chunk 272 optimal weight: 20.0000 chunk 731 optimal weight: 20.0000 chunk 598 optimal weight: 40.0000 chunk 242 optimal weight: 20.0000 chunk 880 optimal weight: 20.0000 chunk 951 optimal weight: 9.9990 chunk 784 optimal weight: 8.9990 chunk 873 optimal weight: 20.0000 chunk 300 optimal weight: 20.0000 chunk 706 optimal weight: 30.0000 overall best weight: 13.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN I 196 GLN ** J 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 GLN N 45 GLN c 44 GLN ** c 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 110 GLN ** e 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 106 ASN r 7 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.092 151769 Z= 0.422 Angle : 0.636 23.479 227451 Z= 0.330 Chirality : 0.041 1.937 29149 Planarity : 0.005 0.064 11892 Dihedral : 14.062 178.463 60459 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.80 % Favored : 97.14 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 0.78 (0.11), residues: 5245 helix: 1.77 (0.12), residues: 1756 sheet: -0.01 (0.15), residues: 1077 loop : -0.07 (0.13), residues: 2412 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10490 Ramachandran restraints generated. 5245 Oldfield, 0 Emsley, 5245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10490 Ramachandran restraints generated. 5245 Oldfield, 0 Emsley, 5245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 4475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 680 time to evaluate : 6.021 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 revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 39 residues processed: 724 average time/residue: 1.2682 time to fit residues: 1620.7933 Evaluate side-chains 675 residues out of total 4475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 636 time to evaluate : 5.984 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 1.0526 time to fit residues: 84.4288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 870 optimal weight: 7.9990 chunk 662 optimal weight: 20.0000 chunk 457 optimal weight: 7.9990 chunk 97 optimal weight: 20.0000 chunk 420 optimal weight: 0.0770 chunk 591 optimal weight: 20.0000 chunk 883 optimal weight: 8.9990 chunk 935 optimal weight: 5.9990 chunk 461 optimal weight: 5.9990 chunk 837 optimal weight: 20.0000 chunk 252 optimal weight: 30.0000 overall best weight: 5.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 GLN N 45 GLN c 77 GLN ** e 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.088 151769 Z= 0.203 Angle : 0.533 23.720 227451 Z= 0.279 Chirality : 0.035 1.911 29149 Planarity : 0.004 0.052 11892 Dihedral : 13.978 178.446 60459 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.40 % Favored : 97.56 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 0.99 (0.12), residues: 5245 helix: 2.00 (0.12), residues: 1751 sheet: 0.06 (0.16), residues: 1075 loop : 0.03 (0.13), residues: 2419 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10490 Ramachandran restraints generated. 5245 Oldfield, 0 Emsley, 5245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10490 Ramachandran restraints generated. 5245 Oldfield, 0 Emsley, 5245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 4475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 697 time to evaluate : 5.932 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 revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 31 residues processed: 718 average time/residue: 1.3604 time to fit residues: 1742.8904 Evaluate side-chains 678 residues out of total 4475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 647 time to evaluate : 6.038 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 1.1574 time to fit residues: 74.6190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 779 optimal weight: 5.9990 chunk 531 optimal weight: 8.9990 chunk 13 optimal weight: 50.0000 chunk 696 optimal weight: 30.0000 chunk 386 optimal weight: 10.0000 chunk 798 optimal weight: 8.9990 chunk 646 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 477 optimal weight: 9.9990 chunk 839 optimal weight: 30.0000 chunk 236 optimal weight: 20.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 GLN N 45 GLN W 54 ASN c 44 GLN c 77 GLN ** c 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 113 GLN ** e 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 151769 Z= 0.281 Angle : 0.553 23.589 227451 Z= 0.289 Chirality : 0.037 1.915 29149 Planarity : 0.004 0.052 11892 Dihedral : 13.944 178.369 60459 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.67 % Favored : 97.29 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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 (0.12), residues: 5245 helix: 1.95 (0.12), residues: 1747 sheet: 0.09 (0.16), residues: 1074 loop : 0.03 (0.13), residues: 2424 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10490 Ramachandran restraints generated. 5245 Oldfield, 0 Emsley, 5245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10490 Ramachandran restraints generated. 5245 Oldfield, 0 Emsley, 5245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 4475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 667 time to evaluate : 5.994 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 revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 26 residues processed: 694 average time/residue: 1.2831 time to fit residues: 1587.6525 Evaluate side-chains 664 residues out of total 4475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 638 time to evaluate : 6.089 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 1.1733 time to fit residues: 65.5111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 314 optimal weight: 20.0000 chunk 842 optimal weight: 6.9990 chunk 184 optimal weight: 40.0000 chunk 549 optimal weight: 20.0000 chunk 230 optimal weight: 20.0000 chunk 936 optimal weight: 5.9990 chunk 777 optimal weight: 7.9990 chunk 433 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 309 optimal weight: 20.0000 chunk 491 optimal weight: 0.3980 overall best weight: 5.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 64 GLN l 64 GLN ** n 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 20 ASN ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 151769 Z= 0.205 Angle : 0.536 23.581 227451 Z= 0.280 Chirality : 0.036 1.919 29149 Planarity : 0.004 0.064 11892 Dihedral : 13.946 178.355 60459 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.65 % Favored : 97.31 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 1.00 (0.12), residues: 5245 helix: 1.98 (0.12), residues: 1745 sheet: 0.12 (0.15), residues: 1090 loop : 0.04 (0.13), residues: 2410 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10490 Ramachandran restraints generated. 5245 Oldfield, 0 Emsley, 5245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10490 Ramachandran restraints generated. 5245 Oldfield, 0 Emsley, 5245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 4475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 670 time to evaluate : 6.085 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: 47 outliers final: 32 residues processed: 688 average time/residue: 1.2028 time to fit residues: 1456.2702 Evaluate side-chains 669 residues out of total 4475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 637 time to evaluate : 5.934 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 1.0320 time to fit residues: 69.2122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 902 optimal weight: 20.0000 chunk 105 optimal weight: 20.0000 chunk 533 optimal weight: 9.9990 chunk 683 optimal weight: 30.0000 chunk 529 optimal weight: 10.0000 chunk 788 optimal weight: 9.9990 chunk 522 optimal weight: 7.9990 chunk 932 optimal weight: 40.0000 chunk 583 optimal weight: 2.9990 chunk 568 optimal weight: 6.9990 chunk 430 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 111 HIS X 45 GLN ** c 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 7 GLN ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 151769 Z= 0.250 Angle : 0.543 23.576 227451 Z= 0.284 Chirality : 0.036 1.917 29149 Planarity : 0.004 0.053 11892 Dihedral : 13.912 178.603 60459 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.65 % Favored : 97.31 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 0.98 (0.12), residues: 5245 helix: 1.93 (0.12), residues: 1748 sheet: 0.11 (0.16), residues: 1083 loop : 0.04 (0.13), residues: 2414 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10490 Ramachandran restraints generated. 5245 Oldfield, 0 Emsley, 5245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10490 Ramachandran restraints generated. 5245 Oldfield, 0 Emsley, 5245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 4475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 656 time to evaluate : 6.115 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: 38 outliers final: 24 residues processed: 675 average time/residue: 1.1921 time to fit residues: 1419.6085 Evaluate side-chains 656 residues out of total 4475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 632 time to evaluate : 6.015 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 1.0045 time to fit residues: 51.8616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 577 optimal weight: 20.0000 chunk 372 optimal weight: 10.0000 chunk 557 optimal weight: 7.9990 chunk 281 optimal weight: 20.0000 chunk 183 optimal weight: 20.0000 chunk 180 optimal weight: 20.0000 chunk 593 optimal weight: 20.0000 chunk 635 optimal weight: 30.0000 chunk 461 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 733 optimal weight: 20.0000 overall best weight: 15.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 17 GLN ** 3 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 GLN K 106 ASN N 45 GLN U 86 GLN X 30 GLN X 45 GLN ** c 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 86 ASN ** e 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 45 HIS p 9 ASN r 7 GLN ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.067 151769 Z= 0.476 Angle : 0.659 23.407 227451 Z= 0.340 Chirality : 0.043 1.911 29149 Planarity : 0.005 0.072 11892 Dihedral : 14.066 179.364 60459 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.13 % Favored : 96.84 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 0.65 (0.11), residues: 5245 helix: 1.59 (0.12), residues: 1750 sheet: -0.05 (0.15), residues: 1095 loop : -0.12 (0.13), residues: 2400 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10490 Ramachandran restraints generated. 5245 Oldfield, 0 Emsley, 5245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10490 Ramachandran restraints generated. 5245 Oldfield, 0 Emsley, 5245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 4475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 627 time to evaluate : 6.001 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: 37 outliers final: 26 residues processed: 637 average time/residue: 1.2562 time to fit residues: 1426.8277 Evaluate side-chains 639 residues out of total 4475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 613 time to evaluate : 5.365 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.9268 time to fit residues: 52.5386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 848 optimal weight: 7.9990 chunk 893 optimal weight: 30.0000 chunk 815 optimal weight: 10.0000 chunk 869 optimal weight: 5.9990 chunk 523 optimal weight: 30.0000 chunk 378 optimal weight: 10.0000 chunk 682 optimal weight: 10.0000 chunk 266 optimal weight: 20.0000 chunk 785 optimal weight: 6.9990 chunk 822 optimal weight: 0.0470 chunk 866 optimal weight: 20.0000 overall best weight: 6.2088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 75 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 GLN ** J 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 GLN U 86 GLN X 45 GLN c 94 HIS ** e 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 151769 Z= 0.218 Angle : 0.546 23.653 227451 Z= 0.285 Chirality : 0.036 1.915 29149 Planarity : 0.004 0.053 11892 Dihedral : 13.989 178.988 60459 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.38 % Favored : 97.58 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: 0.85 (0.12), residues: 5245 helix: 1.80 (0.12), residues: 1745 sheet: 0.05 (0.16), residues: 1060 loop : -0.02 (0.13), residues: 2440 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10490 Ramachandran restraints generated. 5245 Oldfield, 0 Emsley, 5245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10490 Ramachandran restraints generated. 5245 Oldfield, 0 Emsley, 5245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 4475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 658 time to evaluate : 5.999 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: 14 outliers final: 11 residues processed: 665 average time/residue: 1.2157 time to fit residues: 1427.6580 Evaluate side-chains 645 residues out of total 4475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 634 time to evaluate : 5.915 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 1.0250 time to fit residues: 27.3621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 570 optimal weight: 9.9990 chunk 919 optimal weight: 6.9990 chunk 561 optimal weight: 1.9990 chunk 436 optimal weight: 0.0670 chunk 639 optimal weight: 40.0000 chunk 964 optimal weight: 7.9990 chunk 887 optimal weight: 5.9990 chunk 767 optimal weight: 6.9990 chunk 79 optimal weight: 40.0000 chunk 593 optimal weight: 20.0000 chunk 470 optimal weight: 9.9990 overall best weight: 4.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 GLN X 45 GLN ** c 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 7 GLN ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 151769 Z= 0.169 Angle : 0.519 23.537 227451 Z= 0.271 Chirality : 0.034 1.922 29149 Planarity : 0.004 0.059 11892 Dihedral : 13.863 178.561 60459 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.55 % Favored : 97.41 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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 (0.12), residues: 5245 helix: 1.87 (0.12), residues: 1744 sheet: 0.18 (0.16), residues: 1060 loop : 0.05 (0.13), residues: 2441 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10490 Ramachandran restraints generated. 5245 Oldfield, 0 Emsley, 5245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10490 Ramachandran restraints generated. 5245 Oldfield, 0 Emsley, 5245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 4475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 683 time to evaluate : 6.022 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 revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 685 average time/residue: 1.2497 time to fit residues: 1508.3153 Evaluate side-chains 646 residues out of total 4475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 643 time to evaluate : 5.949 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.9980 time to fit residues: 11.8979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 609 optimal weight: 30.0000 chunk 818 optimal weight: 7.9990 chunk 235 optimal weight: 20.0000 chunk 708 optimal weight: 30.0000 chunk 113 optimal weight: 20.0000 chunk 213 optimal weight: 20.0000 chunk 769 optimal weight: 5.9990 chunk 321 optimal weight: 30.0000 chunk 789 optimal weight: 0.7980 chunk 97 optimal weight: 20.0000 chunk 141 optimal weight: 20.0000 overall best weight: 10.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 GLN N 45 GLN X 45 GLN ** c 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 7 GLN ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.039030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.030863 restraints weight = 869657.101| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 1.41 r_work: 0.2665 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.069 151769 Z= 0.345 Angle : 0.590 23.375 227451 Z= 0.306 Chirality : 0.039 1.918 29149 Planarity : 0.004 0.067 11892 Dihedral : 13.899 178.212 60459 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.92 % Favored : 97.04 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 (0.12), residues: 5245 helix: 1.72 (0.12), residues: 1747 sheet: 0.07 (0.16), residues: 1065 loop : 0.02 (0.13), residues: 2433 =============================================================================== Job complete usr+sys time: 28100.38 seconds wall clock time: 497 minutes 50.59 seconds (29870.59 seconds total)