Starting phenix.real_space_refine (version: dev) on Thu Dec 22 20:52:17 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adb_11722/12_2022/7adb_11722_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adb_11722/12_2022/7adb_11722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adb_11722/12_2022/7adb_11722.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adb_11722/12_2022/7adb_11722.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adb_11722/12_2022/7adb_11722_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adb_11722/12_2022/7adb_11722_updated.pdb" } resolution = 4.4 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= 0.013 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "a ARG 30": "NH1" <-> "NH2" Residue "a ARG 92": "NH1" <-> "NH2" Residue "a GLU 108": "OE1" <-> "OE2" Residue "a GLU 226": "OE1" <-> "OE2" Residue "a GLU 244": "OE1" <-> "OE2" Residue "a ARG 299": "NH1" <-> "NH2" Residue "a GLU 309": "OE1" <-> "OE2" Residue "a ARG 347": "NH1" <-> "NH2" Residue "a ARG 366": "NH1" <-> "NH2" Residue "a GLU 375": "OE1" <-> "OE2" Residue "a GLU 397": "OE1" <-> "OE2" Residue "b ARG 30": "NH1" <-> "NH2" Residue "b ARG 92": "NH1" <-> "NH2" Residue "b GLU 108": "OE1" <-> "OE2" Residue "b GLU 226": "OE1" <-> "OE2" Residue "b GLU 244": "OE1" <-> "OE2" Residue "b ARG 299": "NH1" <-> "NH2" Residue "b GLU 309": "OE1" <-> "OE2" Residue "b ARG 347": "NH1" <-> "NH2" Residue "b ARG 366": "NH1" <-> "NH2" Residue "b GLU 375": "OE1" <-> "OE2" Residue "b GLU 397": "OE1" <-> "OE2" Residue "c ARG 30": "NH1" <-> "NH2" Residue "c ARG 92": "NH1" <-> "NH2" Residue "c GLU 108": "OE1" <-> "OE2" Residue "c GLU 226": "OE1" <-> "OE2" Residue "c GLU 244": "OE1" <-> "OE2" Residue "c ARG 299": "NH1" <-> "NH2" Residue "c GLU 309": "OE1" <-> "OE2" Residue "c ARG 347": "NH1" <-> "NH2" Residue "c ARG 366": "NH1" <-> "NH2" Residue "c GLU 375": "OE1" <-> "OE2" Residue "c GLU 397": "OE1" <-> "OE2" Residue "d ARG 30": "NH1" <-> "NH2" Residue "d ARG 92": "NH1" <-> "NH2" Residue "d GLU 108": "OE1" <-> "OE2" Residue "d GLU 226": "OE1" <-> "OE2" Residue "d GLU 244": "OE1" <-> "OE2" Residue "d ARG 299": "NH1" <-> "NH2" Residue "d GLU 309": "OE1" <-> "OE2" Residue "d ARG 347": "NH1" <-> "NH2" Residue "d ARG 366": "NH1" <-> "NH2" Residue "d GLU 375": "OE1" <-> "OE2" Residue "d GLU 397": "OE1" <-> "OE2" Residue "e ARG 30": "NH1" <-> "NH2" Residue "e ARG 92": "NH1" <-> "NH2" Residue "e GLU 108": "OE1" <-> "OE2" Residue "e GLU 226": "OE1" <-> "OE2" Residue "e GLU 244": "OE1" <-> "OE2" Residue "e ARG 299": "NH1" <-> "NH2" Residue "e GLU 309": "OE1" <-> "OE2" Residue "e ARG 347": "NH1" <-> "NH2" Residue "e ARG 366": "NH1" <-> "NH2" Residue "e GLU 375": "OE1" <-> "OE2" Residue "e GLU 397": "OE1" <-> "OE2" Residue "f ARG 30": "NH1" <-> "NH2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "f GLU 108": "OE1" <-> "OE2" Residue "f GLU 226": "OE1" <-> "OE2" Residue "f GLU 244": "OE1" <-> "OE2" Residue "f ARG 299": "NH1" <-> "NH2" Residue "f GLU 309": "OE1" <-> "OE2" Residue "f ARG 347": "NH1" <-> "NH2" Residue "f ARG 366": "NH1" <-> "NH2" Residue "f GLU 375": "OE1" <-> "OE2" Residue "f GLU 397": "OE1" <-> "OE2" Residue "A GLU 25": "OE1" <-> "OE2" Residue "A GLU 42": "OE1" <-> "OE2" Residue "A ARG 51": "NH1" <-> "NH2" Residue "A GLU 98": "OE1" <-> "OE2" Residue "A ARG 119": "NH1" <-> "NH2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A ARG 320": "NH1" <-> "NH2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A GLU 351": "OE1" <-> "OE2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A GLU 383": "OE1" <-> "OE2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A GLU 476": "OE1" <-> "OE2" Residue "U GLU 7": "OE1" <-> "OE2" Residue "U ARG 33": "NH1" <-> "NH2" Residue "U ARG 195": "NH1" <-> "NH2" Residue "U GLU 206": "OE1" <-> "OE2" Residue "U ARG 219": "NH1" <-> "NH2" Residue "U GLU 245": "OE1" <-> "OE2" Residue "U ARG 255": "NH1" <-> "NH2" Residue "U ARG 265": "NH1" <-> "NH2" Residue "U GLU 288": "OE1" <-> "OE2" Residue "U GLU 319": "OE1" <-> "OE2" Residue "V GLU 7": "OE1" <-> "OE2" Residue "V ARG 12": "NH1" <-> "NH2" Residue "V GLU 29": "OE1" <-> "OE2" Residue "V ARG 33": "NH1" <-> "NH2" Residue "V GLU 162": "OE1" <-> "OE2" Residue "W GLU 11": "OE1" <-> "OE2" Residue "W ARG 16": "NH1" <-> "NH2" Residue "W GLU 53": "OE1" <-> "OE2" Residue "W GLU 74": "OE1" <-> "OE2" Residue "X ARG 10": "NH1" <-> "NH2" Residue "X GLU 67": "OE1" <-> "OE2" Residue "X GLU 119": "OE1" <-> "OE2" Residue "X ARG 151": "NH1" <-> "NH2" Residue "X ARG 180": "NH1" <-> "NH2" Residue "X PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 264": "OE1" <-> "OE2" Residue "X ARG 268": "NH1" <-> "NH2" Residue "X GLU 308": "OE1" <-> "OE2" Residue "X GLU 349": "OE1" <-> "OE2" Residue "X ARG 371": "NH1" <-> "NH2" Residue "X GLU 413": "OE1" <-> "OE2" Residue "X ARG 451": "NH1" <-> "NH2" Residue "X GLU 504": "OE1" <-> "OE2" Residue "X GLU 546": "OE1" <-> "OE2" Residue "X GLU 565": "OE1" <-> "OE2" Residue "X ARG 647": "NH1" <-> "NH2" Residue "X GLU 825": "OE1" <-> "OE2" Residue "X GLU 898": "OE1" <-> "OE2" Residue "X ARG 903": "NH1" <-> "NH2" Residue "X GLU 940": "OE1" <-> "OE2" Residue "X GLU 963": "OE1" <-> "OE2" Residue "X ARG 996": "NH1" <-> "NH2" Residue "X ARG 1034": "NH1" <-> "NH2" Residue "X GLU 1089": "OE1" <-> "OE2" Residue "X ARG 1106": "NH1" <-> "NH2" Residue "X GLU 1167": "OE1" <-> "OE2" Residue "X ARG 1171": "NH1" <-> "NH2" Residue "X GLU 1272": "OE1" <-> "OE2" Residue "X GLU 1279": "OE1" <-> "OE2" Residue "X GLU 1329": "OE1" <-> "OE2" Residue "X GLU 1338": "OE1" <-> "OE2" Residue "Y GLU 37": "OE1" <-> "OE2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 53": "NH1" <-> "NH2" Residue "Y GLU 69": "OE1" <-> "OE2" Residue "Y ARG 101": "NH1" <-> "NH2" Residue "Y ARG 133": "NH1" <-> "NH2" Residue "Y ARG 314": "NH1" <-> "NH2" Residue "Y GLU 386": "OE1" <-> "OE2" Residue "Y GLU 402": "OE1" <-> "OE2" Residue "Y ARG 425": "NH1" <-> "NH2" Residue "Y GLU 443": "OE1" <-> "OE2" Residue "Y ARG 515": "NH1" <-> "NH2" Residue "Y ARG 634": "NH1" <-> "NH2" Residue "Y GLU 663": "OE1" <-> "OE2" Residue "Y GLU 677": "OE1" <-> "OE2" Residue "Y ARG 692": "NH1" <-> "NH2" Residue "Y GLU 765": "OE1" <-> "OE2" Residue "Y ARG 836": "NH1" <-> "NH2" Residue "Y GLU 866": "OE1" <-> "OE2" Residue "Y GLU 874": "OE1" <-> "OE2" Residue "Y GLU 913": "OE1" <-> "OE2" Residue "Y ARG 933": "NH1" <-> "NH2" Residue "Y ARG 943": "NH1" <-> "NH2" Residue "Y GLU 947": "OE1" <-> "OE2" Residue "Y ARG 1036": "NH1" <-> "NH2" Residue "Y GLU 1052": "OE1" <-> "OE2" Residue "Y GLU 1146": "OE1" <-> "OE2" Residue "Y ARG 1148": "NH1" <-> "NH2" Residue "Y GLU 1187": "OE1" <-> "OE2" Residue "Y GLU 1205": "OE1" <-> "OE2" Residue "Y GLU 1236": "OE1" <-> "OE2" Residue "Y ARG 1258": "NH1" <-> "NH2" Residue "Y GLU 1327": "OE1" <-> "OE2" Residue "Y ARG 1345": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 51330 Number of models: 1 Model: "" Number of chains: 26 Chain: "a" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 398} Chain: "b" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 398} Chain: "c" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 398} Chain: "d" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 398} Chain: "e" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 398} Chain: "f" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 398} Chain: "A" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3852 Classifications: {'peptide': 495} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 480} Chain: "U" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2510 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 305} Chain: "V" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1828 Classifications: {'peptide': 235} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 225} Chain: "W" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "X" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "Y" Number of atoms: 10545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1358, 10545 Classifications: {'peptide': 1358} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1302} Chain: "K" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 497 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain breaks: 1 Chain: "L" Number of atoms: 682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 682 Classifications: {'DNA': 34} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 33} Chain: "R" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 364 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 8, 'rna3p_pyr': 8} Link IDs: {'rna2p': 1, 'rna3p': 15} Chain breaks: 1 Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "f" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "f" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 39513 SG CYS Y 70 94.114 111.046 92.022 1.00164.10 S ATOM 39527 SG CYS Y 72 93.362 107.519 92.259 1.00173.13 S ATOM 39635 SG CYS Y 85 90.800 109.992 92.691 1.00119.58 S ATOM 39659 SG CYS Y 88 93.949 110.750 95.561 1.00146.28 S ATOM 45347 SG CYS Y 814 105.619 176.997 88.573 1.00 80.35 S ATOM 45912 SG CYS Y 888 108.351 173.231 89.446 1.00 84.15 S ATOM 45963 SG CYS Y 895 104.963 173.401 87.191 1.00 81.30 S ATOM 45984 SG CYS Y 898 108.341 175.591 86.670 1.00 64.63 S Time building chain proxies: 26.05, per 1000 atoms: 0.51 Number of scatterers: 51330 At special positions: 0 Unit cell: (197.16, 217, 163.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 S 223 16.00 P 84 15.00 Mg 6 11.99 F 15 9.00 O 10026 8.00 N 9072 7.00 C 31897 6.00 Be 5 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.14 Conformation dependent library (CDL) restraints added in 7.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Y1502 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 85 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 88 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 72 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 70 " pdb=" ZN Y1503 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 888 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 898 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 895 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 814 " Number of angles added : 12 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11748 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 231 helices and 55 sheets defined 35.4% alpha, 11.5% beta 29 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 17.52 Creating SS restraints... Processing helix chain 'a' and resid 4 through 7 No H-bonds generated for 'chain 'a' and resid 4 through 7' Processing helix chain 'a' and resid 11 through 20 Processing helix chain 'a' and resid 26 through 28 No H-bonds generated for 'chain 'a' and resid 26 through 28' Processing helix chain 'a' and resid 31 through 44 Processing helix chain 'a' and resid 83 through 89 Processing helix chain 'a' and resid 124 through 127 Processing helix chain 'a' and resid 156 through 165 Processing helix chain 'a' and resid 185 through 198 Processing helix chain 'a' and resid 213 through 220 Processing helix chain 'a' and resid 236 through 255 Processing helix chain 'a' and resid 267 through 277 Processing helix chain 'a' and resid 286 through 288 No H-bonds generated for 'chain 'a' and resid 286 through 288' Processing helix chain 'a' and resid 292 through 302 removed outlier: 4.792A pdb=" N ARG a 296 " --> pdb=" O ALA a 293 " (cutoff:3.500A) Proline residue: a 297 - end of helix Processing helix chain 'a' and resid 327 through 336 Processing helix chain 'a' and resid 368 through 371 Processing helix chain 'a' and resid 374 through 387 Processing helix chain 'a' and resid 393 through 404 Processing helix chain 'a' and resid 409 through 416 Processing helix chain 'b' and resid 4 through 7 No H-bonds generated for 'chain 'b' and resid 4 through 7' Processing helix chain 'b' and resid 11 through 20 Processing helix chain 'b' and resid 26 through 28 No H-bonds generated for 'chain 'b' and resid 26 through 28' Processing helix chain 'b' and resid 31 through 44 Processing helix chain 'b' and resid 83 through 89 Processing helix chain 'b' and resid 124 through 127 Processing helix chain 'b' and resid 156 through 165 Processing helix chain 'b' and resid 185 through 198 Processing helix chain 'b' and resid 213 through 220 Processing helix chain 'b' and resid 236 through 255 Processing helix chain 'b' and resid 267 through 277 Processing helix chain 'b' and resid 286 through 288 No H-bonds generated for 'chain 'b' and resid 286 through 288' Processing helix chain 'b' and resid 292 through 302 removed outlier: 4.792A pdb=" N ARG b 296 " --> pdb=" O ALA b 293 " (cutoff:3.500A) Proline residue: b 297 - end of helix Processing helix chain 'b' and resid 327 through 336 Processing helix chain 'b' and resid 368 through 371 Processing helix chain 'b' and resid 374 through 387 Processing helix chain 'b' and resid 393 through 404 Processing helix chain 'b' and resid 409 through 416 Processing helix chain 'c' and resid 4 through 7 No H-bonds generated for 'chain 'c' and resid 4 through 7' Processing helix chain 'c' and resid 11 through 20 Processing helix chain 'c' and resid 26 through 28 No H-bonds generated for 'chain 'c' and resid 26 through 28' Processing helix chain 'c' and resid 31 through 44 Processing helix chain 'c' and resid 83 through 89 Processing helix chain 'c' and resid 124 through 127 Processing helix chain 'c' and resid 156 through 165 Processing helix chain 'c' and resid 185 through 198 Processing helix chain 'c' and resid 213 through 220 Processing helix chain 'c' and resid 236 through 255 Processing helix chain 'c' and resid 267 through 277 Processing helix chain 'c' and resid 286 through 288 No H-bonds generated for 'chain 'c' and resid 286 through 288' Processing helix chain 'c' and resid 292 through 302 removed outlier: 4.792A pdb=" N ARG c 296 " --> pdb=" O ALA c 293 " (cutoff:3.500A) Proline residue: c 297 - end of helix Processing helix chain 'c' and resid 327 through 336 Processing helix chain 'c' and resid 368 through 371 Processing helix chain 'c' and resid 374 through 387 Processing helix chain 'c' and resid 393 through 404 Processing helix chain 'c' and resid 409 through 416 Processing helix chain 'd' and resid 4 through 7 No H-bonds generated for 'chain 'd' and resid 4 through 7' Processing helix chain 'd' and resid 11 through 20 Processing helix chain 'd' and resid 26 through 28 No H-bonds generated for 'chain 'd' and resid 26 through 28' Processing helix chain 'd' and resid 31 through 44 Processing helix chain 'd' and resid 83 through 89 Processing helix chain 'd' and resid 124 through 127 Processing helix chain 'd' and resid 156 through 165 Processing helix chain 'd' and resid 185 through 198 Processing helix chain 'd' and resid 213 through 220 Processing helix chain 'd' and resid 236 through 255 Processing helix chain 'd' and resid 267 through 277 Processing helix chain 'd' and resid 286 through 288 No H-bonds generated for 'chain 'd' and resid 286 through 288' Processing helix chain 'd' and resid 292 through 302 removed outlier: 4.793A pdb=" N ARG d 296 " --> pdb=" O ALA d 293 " (cutoff:3.500A) Proline residue: d 297 - end of helix Processing helix chain 'd' and resid 327 through 336 Processing helix chain 'd' and resid 368 through 371 Processing helix chain 'd' and resid 374 through 387 Processing helix chain 'd' and resid 393 through 404 Processing helix chain 'd' and resid 409 through 416 Processing helix chain 'e' and resid 4 through 7 No H-bonds generated for 'chain 'e' and resid 4 through 7' Processing helix chain 'e' and resid 11 through 20 Processing helix chain 'e' and resid 26 through 28 No H-bonds generated for 'chain 'e' and resid 26 through 28' Processing helix chain 'e' and resid 31 through 44 Processing helix chain 'e' and resid 83 through 89 Processing helix chain 'e' and resid 124 through 127 Processing helix chain 'e' and resid 156 through 165 Processing helix chain 'e' and resid 185 through 198 Processing helix chain 'e' and resid 213 through 220 Processing helix chain 'e' and resid 236 through 255 Processing helix chain 'e' and resid 267 through 277 Processing helix chain 'e' and resid 286 through 288 No H-bonds generated for 'chain 'e' and resid 286 through 288' Processing helix chain 'e' and resid 292 through 302 removed outlier: 4.792A pdb=" N ARG e 296 " --> pdb=" O ALA e 293 " (cutoff:3.500A) Proline residue: e 297 - end of helix Processing helix chain 'e' and resid 327 through 336 Processing helix chain 'e' and resid 368 through 371 Processing helix chain 'e' and resid 374 through 387 Processing helix chain 'e' and resid 393 through 404 Processing helix chain 'e' and resid 409 through 416 Processing helix chain 'f' and resid 4 through 7 No H-bonds generated for 'chain 'f' and resid 4 through 7' Processing helix chain 'f' and resid 11 through 20 Processing helix chain 'f' and resid 26 through 28 No H-bonds generated for 'chain 'f' and resid 26 through 28' Processing helix chain 'f' and resid 31 through 44 Processing helix chain 'f' and resid 83 through 89 Processing helix chain 'f' and resid 124 through 127 Processing helix chain 'f' and resid 156 through 165 Processing helix chain 'f' and resid 185 through 198 Processing helix chain 'f' and resid 213 through 220 Processing helix chain 'f' and resid 236 through 255 Processing helix chain 'f' and resid 267 through 277 Processing helix chain 'f' and resid 286 through 288 No H-bonds generated for 'chain 'f' and resid 286 through 288' Processing helix chain 'f' and resid 292 through 302 removed outlier: 4.793A pdb=" N ARG f 296 " --> pdb=" O ALA f 293 " (cutoff:3.500A) Proline residue: f 297 - end of helix Processing helix chain 'f' and resid 327 through 336 Processing helix chain 'f' and resid 368 through 371 Processing helix chain 'f' and resid 374 through 387 Processing helix chain 'f' and resid 393 through 404 Processing helix chain 'f' and resid 409 through 416 Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 20 through 38 removed outlier: 3.760A pdb=" N LYS A 37 " --> pdb=" O THR A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 104 through 132 Processing helix chain 'A' and resid 202 through 212 removed outlier: 3.907A pdb=" N ILE A 206 " --> pdb=" O PRO A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 250 No H-bonds generated for 'chain 'A' and resid 247 through 250' Processing helix chain 'A' and resid 258 through 266 Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 314 through 317 No H-bonds generated for 'chain 'A' and resid 314 through 317' Processing helix chain 'A' and resid 320 through 331 removed outlier: 6.304A pdb=" N ASN A 324 " --> pdb=" O ASN A 321 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU A 327 " --> pdb=" O ASN A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 425 Processing helix chain 'A' and resid 432 through 435 No H-bonds generated for 'chain 'A' and resid 432 through 435' Processing helix chain 'A' and resid 442 through 451 Processing helix chain 'A' and resid 458 through 461 Processing helix chain 'A' and resid 475 through 489 Processing helix chain 'U' and resid 35 through 49 Processing helix chain 'U' and resid 78 through 87 Processing helix chain 'U' and resid 112 through 114 No H-bonds generated for 'chain 'U' and resid 112 through 114' Processing helix chain 'U' and resid 213 through 232 Processing helix chain 'U' and resid 257 through 259 No H-bonds generated for 'chain 'U' and resid 257 through 259' Processing helix chain 'U' and resid 265 through 272 Processing helix chain 'U' and resid 278 through 283 removed outlier: 4.808A pdb=" N GLN U 283 " --> pdb=" O GLY U 279 " (cutoff:3.500A) Processing helix chain 'U' and resid 286 through 290 removed outlier: 4.315A pdb=" N LEU U 290 " --> pdb=" O VAL U 287 " (cutoff:3.500A) Processing helix chain 'U' and resid 298 through 308 removed outlier: 3.669A pdb=" N LEU U 307 " --> pdb=" O ILE U 303 " (cutoff:3.500A) Processing helix chain 'V' and resid 19 through 21 No H-bonds generated for 'chain 'V' and resid 19 through 21' Processing helix chain 'V' and resid 35 through 48 Processing helix chain 'V' and resid 78 through 86 Processing helix chain 'V' and resid 112 through 114 No H-bonds generated for 'chain 'V' and resid 112 through 114' Processing helix chain 'V' and resid 155 through 162 Processing helix chain 'V' and resid 213 through 230 removed outlier: 4.940A pdb=" N ALA V 230 " --> pdb=" O GLU V 226 " (cutoff:3.500A) Processing helix chain 'W' and resid 7 through 12 removed outlier: 3.966A pdb=" N LYS W 12 " --> pdb=" O ASP W 8 " (cutoff:3.500A) Processing helix chain 'W' and resid 18 through 31 Processing helix chain 'W' and resid 46 through 56 Processing helix chain 'W' and resid 61 through 79 Processing helix chain 'X' and resid 5 through 9 Processing helix chain 'X' and resid 29 through 38 Processing helix chain 'X' and resid 50 through 56 Processing helix chain 'X' and resid 82 through 88 Processing helix chain 'X' and resid 164 through 166 No H-bonds generated for 'chain 'X' and resid 164 through 166' Processing helix chain 'X' and resid 206 through 213 removed outlier: 4.187A pdb=" N LEU X 213 " --> pdb=" O ILE X 209 " (cutoff:3.500A) Processing helix chain 'X' and resid 217 through 223 Processing helix chain 'X' and resid 243 through 246 removed outlier: 3.681A pdb=" N LEU X 246 " --> pdb=" O PRO X 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 243 through 246' Processing helix chain 'X' and resid 271 through 280 Processing helix chain 'X' and resid 289 through 294 removed outlier: 3.557A pdb=" N ALA X 293 " --> pdb=" O VAL X 289 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY X 294 " --> pdb=" O GLU X 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 289 through 294' Processing helix chain 'X' and resid 319 through 328 Processing helix chain 'X' and resid 347 through 352 Processing helix chain 'X' and resid 359 through 370 Processing helix chain 'X' and resid 380 through 388 Processing helix chain 'X' and resid 399 through 408 Processing helix chain 'X' and resid 422 through 437 Processing helix chain 'X' and resid 448 through 450 No H-bonds generated for 'chain 'X' and resid 448 through 450' Processing helix chain 'X' and resid 456 through 479 removed outlier: 3.565A pdb=" N ARG X 470 " --> pdb=" O VAL X 466 " (cutoff:3.500A) Processing helix chain 'X' and resid 496 through 507 Processing helix chain 'X' and resid 520 through 527 Processing helix chain 'X' and resid 545 through 548 No H-bonds generated for 'chain 'X' and resid 545 through 548' Processing helix chain 'X' and resid 552 through 554 No H-bonds generated for 'chain 'X' and resid 552 through 554' Processing helix chain 'X' and resid 665 through 667 No H-bonds generated for 'chain 'X' and resid 665 through 667' Processing helix chain 'X' and resid 671 through 673 No H-bonds generated for 'chain 'X' and resid 671 through 673' Processing helix chain 'X' and resid 676 through 687 removed outlier: 3.706A pdb=" N ARG X 687 " --> pdb=" O ALA X 683 " (cutoff:3.500A) Processing helix chain 'X' and resid 704 through 711 removed outlier: 3.924A pdb=" N VAL X 708 " --> pdb=" O GLU X 705 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ALA X 709 " --> pdb=" O ARG X 706 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP X 711 " --> pdb=" O VAL X 708 " (cutoff:3.500A) Processing helix chain 'X' and resid 820 through 824 Processing helix chain 'X' and resid 897 through 905 Processing helix chain 'X' and resid 943 through 978 Processing helix chain 'X' and resid 983 through 989 Processing helix chain 'X' and resid 994 through 996 No H-bonds generated for 'chain 'X' and resid 994 through 996' Processing helix chain 'X' and resid 1004 through 1037 removed outlier: 4.862A pdb=" N ASN X1009 " --> pdb=" O GLU X1005 " (cutoff:3.500A) Processing helix chain 'X' and resid 1100 through 1102 No H-bonds generated for 'chain 'X' and resid 1100 through 1102' Processing helix chain 'X' and resid 1110 through 1133 Processing helix chain 'X' and resid 1138 through 1149 Processing helix chain 'X' and resid 1168 through 1178 removed outlier: 4.534A pdb=" N LYS X1178 " --> pdb=" O GLU X1174 " (cutoff:3.500A) Processing helix chain 'X' and resid 1193 through 1201 Processing helix chain 'X' and resid 1239 through 1242 No H-bonds generated for 'chain 'X' and resid 1239 through 1242' Processing helix chain 'X' and resid 1272 through 1280 Processing helix chain 'X' and resid 1284 through 1291 Processing helix chain 'X' and resid 1298 through 1309 Processing helix chain 'X' and resid 1321 through 1331 Processing helix chain 'Y' and resid 27 through 33 Processing helix chain 'Y' and resid 95 through 100 Processing helix chain 'Y' and resid 114 through 116 No H-bonds generated for 'chain 'Y' and resid 114 through 116' Processing helix chain 'Y' and resid 124 through 127 No H-bonds generated for 'chain 'Y' and resid 124 through 127' Processing helix chain 'Y' and resid 132 through 139 Processing helix chain 'Y' and resid 162 through 169 Processing helix chain 'Y' and resid 182 through 190 Processing helix chain 'Y' and resid 195 through 207 Processing helix chain 'Y' and resid 212 through 229 Processing helix chain 'Y' and resid 234 through 237 Processing helix chain 'Y' and resid 247 through 249 No H-bonds generated for 'chain 'Y' and resid 247 through 249' Processing helix chain 'Y' and resid 264 through 284 removed outlier: 3.816A pdb=" N LEU Y 268 " --> pdb=" O ASP Y 264 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP Y 284 " --> pdb=" O LYS Y 280 " (cutoff:3.500A) Processing helix chain 'Y' and resid 289 through 307 Processing helix chain 'Y' and resid 337 through 340 No H-bonds generated for 'chain 'Y' and resid 337 through 340' Processing helix chain 'Y' and resid 370 through 376 Processing helix chain 'Y' and resid 378 through 387 Processing helix chain 'Y' and resid 394 through 403 Processing helix chain 'Y' and resid 406 through 415 removed outlier: 4.420A pdb=" N ASP Y 410 " --> pdb=" O VAL Y 407 " (cutoff:3.500A) Processing helix chain 'Y' and resid 431 through 433 No H-bonds generated for 'chain 'Y' and resid 431 through 433' Processing helix chain 'Y' and resid 451 through 457 removed outlier: 4.055A pdb=" N ALA Y 455 " --> pdb=" O PRO Y 451 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA Y 456 " --> pdb=" O LEU Y 452 " (cutoff:3.500A) Processing helix chain 'Y' and resid 474 through 483 Processing helix chain 'Y' and resid 504 through 514 Processing helix chain 'Y' and resid 530 through 539 Processing helix chain 'Y' and resid 574 through 581 removed outlier: 4.050A pdb=" N MET Y 581 " --> pdb=" O ALA Y 577 " (cutoff:3.500A) Processing helix chain 'Y' and resid 598 through 611 Processing helix chain 'Y' and resid 615 through 633 removed outlier: 4.375A pdb=" N ILE Y 619 " --> pdb=" O LYS Y 615 " (cutoff:3.500A) Processing helix chain 'Y' and resid 641 through 643 No H-bonds generated for 'chain 'Y' and resid 641 through 643' Processing helix chain 'Y' and resid 648 through 669 removed outlier: 4.212A pdb=" N HIS Y 651 " --> pdb=" O GLU Y 648 " (cutoff:3.500A) Processing helix chain 'Y' and resid 675 through 701 removed outlier: 3.957A pdb=" N ASP Y 684 " --> pdb=" O ASN Y 680 " (cutoff:3.500A) Processing helix chain 'Y' and resid 723 through 726 No H-bonds generated for 'chain 'Y' and resid 723 through 726' Processing helix chain 'Y' and resid 734 through 741 Processing helix chain 'Y' and resid 769 through 803 removed outlier: 4.007A pdb=" N LYS Y 781 " --> pdb=" O HIS Y 777 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY Y 782 " --> pdb=" O GLY Y 778 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR Y 786 " --> pdb=" O GLY Y 782 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA Y 787 " --> pdb=" O LEU Y 783 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ALA Y 791 " --> pdb=" O ALA Y 787 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN Y 792 " --> pdb=" O LEU Y 788 " (cutoff:3.500A) Processing helix chain 'Y' and resid 835 through 839 Processing helix chain 'Y' and resid 866 through 875 Processing helix chain 'Y' and resid 896 through 899 No H-bonds generated for 'chain 'Y' and resid 896 through 899' Processing helix chain 'Y' and resid 915 through 928 Proline residue: Y 926 - end of helix Processing helix chain 'Y' and resid 1138 through 1146 Processing helix chain 'Y' and resid 1217 through 1224 removed outlier: 3.912A pdb=" N ARG Y1222 " --> pdb=" O HIS Y1218 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1226 through 1244 removed outlier: 3.814A pdb=" N GLN Y1244 " --> pdb=" O VAL Y1240 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1250 through 1262 removed outlier: 3.679A pdb=" N ARG Y1262 " --> pdb=" O ARG Y1258 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1282 through 1294 Processing helix chain 'Y' and resid 1309 through 1314 removed outlier: 3.668A pdb=" N SER Y1313 " --> pdb=" O ILE Y1309 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU Y1314 " --> pdb=" O THR Y1310 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 1309 through 1314' Processing helix chain 'Y' and resid 1320 through 1324 Processing helix chain 'Y' and resid 1328 through 1338 Processing helix chain 'Y' and resid 1348 through 1353 Processing helix chain 'Y' and resid 1362 through 1372 Processing sheet with id= A, first strand: chain 'a' and resid 49 through 53 removed outlier: 6.463A pdb=" N LYS a 100 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL a 116 " --> pdb=" O LYS a 100 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'a' and resid 54 through 57 Processing sheet with id= C, first strand: chain 'a' and resid 341 through 345 removed outlier: 8.102A pdb=" N GLY a 174 " --> pdb=" O LEU a 313 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE a 315 " --> pdb=" O GLY a 174 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE a 176 " --> pdb=" O ILE a 315 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA a 317 " --> pdb=" O ILE a 176 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA a 178 " --> pdb=" O ALA a 317 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ALA a 319 " --> pdb=" O ALA a 178 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL a 203 " --> pdb=" O ILE a 261 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N LEU a 263 " --> pdb=" O VAL a 203 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N MET a 205 " --> pdb=" O LEU a 263 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLU a 226 " --> pdb=" O VAL a 206 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LEU a 208 " --> pdb=" O GLU a 226 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL a 228 " --> pdb=" O LEU a 208 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'b' and resid 49 through 53 removed outlier: 6.464A pdb=" N LYS b 100 " --> pdb=" O VAL b 116 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL b 116 " --> pdb=" O LYS b 100 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'b' and resid 54 through 57 Processing sheet with id= F, first strand: chain 'b' and resid 341 through 345 removed outlier: 8.101A pdb=" N GLY b 174 " --> pdb=" O LEU b 313 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE b 315 " --> pdb=" O GLY b 174 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE b 176 " --> pdb=" O ILE b 315 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA b 317 " --> pdb=" O ILE b 176 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ALA b 178 " --> pdb=" O ALA b 317 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ALA b 319 " --> pdb=" O ALA b 178 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL b 203 " --> pdb=" O ILE b 261 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N LEU b 263 " --> pdb=" O VAL b 203 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N MET b 205 " --> pdb=" O LEU b 263 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU b 226 " --> pdb=" O VAL b 206 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LEU b 208 " --> pdb=" O GLU b 226 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL b 228 " --> pdb=" O LEU b 208 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'c' and resid 49 through 53 removed outlier: 6.464A pdb=" N LYS c 100 " --> pdb=" O VAL c 116 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL c 116 " --> pdb=" O LYS c 100 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'c' and resid 54 through 57 Processing sheet with id= I, first strand: chain 'c' and resid 341 through 345 removed outlier: 8.102A pdb=" N GLY c 174 " --> pdb=" O LEU c 313 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE c 315 " --> pdb=" O GLY c 174 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE c 176 " --> pdb=" O ILE c 315 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA c 317 " --> pdb=" O ILE c 176 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ALA c 178 " --> pdb=" O ALA c 317 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ALA c 319 " --> pdb=" O ALA c 178 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N VAL c 203 " --> pdb=" O ILE c 261 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N LEU c 263 " --> pdb=" O VAL c 203 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N MET c 205 " --> pdb=" O LEU c 263 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU c 226 " --> pdb=" O VAL c 206 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LEU c 208 " --> pdb=" O GLU c 226 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL c 228 " --> pdb=" O LEU c 208 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'd' and resid 49 through 53 removed outlier: 6.464A pdb=" N LYS d 100 " --> pdb=" O VAL d 116 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL d 116 " --> pdb=" O LYS d 100 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'd' and resid 54 through 57 Processing sheet with id= L, first strand: chain 'd' and resid 341 through 345 removed outlier: 8.102A pdb=" N GLY d 174 " --> pdb=" O LEU d 313 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE d 315 " --> pdb=" O GLY d 174 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE d 176 " --> pdb=" O ILE d 315 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA d 317 " --> pdb=" O ILE d 176 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ALA d 178 " --> pdb=" O ALA d 317 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ALA d 319 " --> pdb=" O ALA d 178 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL d 203 " --> pdb=" O ILE d 261 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N LEU d 263 " --> pdb=" O VAL d 203 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N MET d 205 " --> pdb=" O LEU d 263 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLU d 226 " --> pdb=" O VAL d 206 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LEU d 208 " --> pdb=" O GLU d 226 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL d 228 " --> pdb=" O LEU d 208 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'e' and resid 49 through 53 removed outlier: 6.464A pdb=" N LYS e 100 " --> pdb=" O VAL e 116 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL e 116 " --> pdb=" O LYS e 100 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'e' and resid 54 through 57 Processing sheet with id= O, first strand: chain 'e' and resid 341 through 345 removed outlier: 8.102A pdb=" N GLY e 174 " --> pdb=" O LEU e 313 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE e 315 " --> pdb=" O GLY e 174 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE e 176 " --> pdb=" O ILE e 315 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA e 317 " --> pdb=" O ILE e 176 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA e 178 " --> pdb=" O ALA e 317 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ALA e 319 " --> pdb=" O ALA e 178 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N VAL e 203 " --> pdb=" O ILE e 261 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N LEU e 263 " --> pdb=" O VAL e 203 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N MET e 205 " --> pdb=" O LEU e 263 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLU e 226 " --> pdb=" O VAL e 206 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LEU e 208 " --> pdb=" O GLU e 226 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL e 228 " --> pdb=" O LEU e 208 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'f' and resid 49 through 53 removed outlier: 6.464A pdb=" N LYS f 100 " --> pdb=" O VAL f 116 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL f 116 " --> pdb=" O LYS f 100 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'f' and resid 54 through 57 Processing sheet with id= R, first strand: chain 'f' and resid 341 through 345 removed outlier: 8.102A pdb=" N GLY f 174 " --> pdb=" O LEU f 313 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE f 315 " --> pdb=" O GLY f 174 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE f 176 " --> pdb=" O ILE f 315 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA f 317 " --> pdb=" O ILE f 176 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA f 178 " --> pdb=" O ALA f 317 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ALA f 319 " --> pdb=" O ALA f 178 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N VAL f 203 " --> pdb=" O ILE f 261 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N LEU f 263 " --> pdb=" O VAL f 203 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N MET f 205 " --> pdb=" O LEU f 263 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLU f 226 " --> pdb=" O VAL f 206 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LEU f 208 " --> pdb=" O GLU f 226 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL f 228 " --> pdb=" O LEU f 208 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A' and resid 178 through 181 removed outlier: 6.767A pdb=" N SER A 151 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N VAL A 145 " --> pdb=" O ASN A 149 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ASN A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 270 through 275 removed outlier: 5.997A pdb=" N LYS A 239 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE A 223 " --> pdb=" O LYS A 239 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 293 through 299 removed outlier: 4.021A pdb=" N ALA A 294 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ALA A 308 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE A 296 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASP A 306 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N VAL A 298 " --> pdb=" O THR A 304 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N THR A 304 " --> pdb=" O VAL A 298 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'U' and resid 24 through 28 Processing sheet with id= W, first strand: chain 'U' and resid 170 through 172 removed outlier: 6.790A pdb=" N LYS U 145 " --> pdb=" O THR U 57 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL U 59 " --> pdb=" O ARG U 143 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG U 143 " --> pdb=" O VAL U 59 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ILE U 61 " --> pdb=" O SER U 141 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N SER U 141 " --> pdb=" O ILE U 61 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'U' and resid 90 through 92 Processing sheet with id= Y, first strand: chain 'U' and resid 108 through 111 Processing sheet with id= Z, first strand: chain 'V' and resid 23 through 28 Processing sheet with id= AA, first strand: chain 'V' and resid 90 through 92 Processing sheet with id= AB, first strand: chain 'V' and resid 97 through 101 removed outlier: 6.094A pdb=" N GLN V 147 " --> pdb=" O VAL V 56 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL V 56 " --> pdb=" O GLN V 147 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'V' and resid 109 through 111 Processing sheet with id= AD, first strand: chain 'X' and resid 93 through 95 Processing sheet with id= AE, first strand: chain 'X' and resid 118 through 123 removed outlier: 4.096A pdb=" N SER X 72 " --> pdb=" O LYS X 99 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ARG X 101 " --> pdb=" O TYR X 70 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TYR X 70 " --> pdb=" O ARG X 101 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL X 103 " --> pdb=" O LEU X 68 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LEU X 68 " --> pdb=" O VAL X 103 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'X' and resid 148 through 151 Processing sheet with id= AG, first strand: chain 'X' and resid 154 through 160 removed outlier: 5.995A pdb=" N TYR X 172 " --> pdb=" O PHE X 188 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE X 188 " --> pdb=" O TYR X 172 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'X' and resid 228 through 231 Processing sheet with id= AI, first strand: chain 'X' and resid 529 through 531 removed outlier: 4.043A pdb=" N SER X 574 " --> pdb=" O GLU X 562 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLU X 562 " --> pdb=" O SER X 574 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'X' and resid 603 through 606 Processing sheet with id= AK, first strand: chain 'X' and resid 634 through 637 Processing sheet with id= AL, first strand: chain 'X' and resid 748 through 752 removed outlier: 3.809A pdb=" N TYR X 726 " --> pdb=" O VAL X 733 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LYS X 735 " --> pdb=" O VAL X 724 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N VAL X 724 " --> pdb=" O LYS X 735 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'X' and resid 1227 through 1232 removed outlier: 6.799A pdb=" N ILE X1096 " --> pdb=" O ALA X 803 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'X' and resid 830 through 839 removed outlier: 3.899A pdb=" N ASP X 930 " --> pdb=" O TYR X1053 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ALA X1055 " --> pdb=" O VAL X 928 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL X 928 " --> pdb=" O ALA X1055 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'X' and resid 1065 through 1067 Processing sheet with id= AP, first strand: chain 'X' and resid 255 through 257 removed outlier: 6.354A pdb=" N ALA X 257 " --> pdb=" O VAL X 261 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N VAL X 261 " --> pdb=" O ALA X 257 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'Y' and resid 104 through 106 Processing sheet with id= AR, first strand: chain 'Y' and resid 143 through 145 Processing sheet with id= AS, first strand: chain 'Y' and resid 350 through 354 Processing sheet with id= AT, first strand: chain 'Y' and resid 355 through 358 removed outlier: 6.327A pdb=" N ILE Y 447 " --> pdb=" O THR Y 356 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLY Y 358 " --> pdb=" O ILE Y 447 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU Y 449 " --> pdb=" O GLY Y 358 " (cutoff:3.500A) No H-bonds generated for sheet with id= AT Processing sheet with id= AU, first strand: chain 'Y' and resid 548 through 557 Processing sheet with id= AV, first strand: chain 'Y' and resid 819 through 822 removed outlier: 3.631A pdb=" N VAL Y 880 " --> pdb=" O MET Y 822 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'Y' and resid 957 through 961 removed outlier: 3.651A pdb=" N GLU Y 981 " --> pdb=" O SER Y 961 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU Y 993 " --> pdb=" O LEU Y 984 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'Y' and resid 965 through 967 Processing sheet with id= AY, first strand: chain 'Y' and resid 1033 through 1035 removed outlier: 3.702A pdb=" N GLY Y1033 " --> pdb=" O ILE Y1115 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL Y1035 " --> pdb=" O VAL Y1113 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL Y1113 " --> pdb=" O VAL Y1035 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'Y' and resid 1059 through 1061 removed outlier: 3.712A pdb=" N ALA Y1105 " --> pdb=" O VAL Y1061 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'Y' and resid 1077 through 1079 Processing sheet with id= BB, first strand: chain 'Y' and resid 1162 through 1164 Processing sheet with id= BC, first strand: chain 'Y' and resid 1279 through 1281 1688 hydrogen bonds defined for protein. 4668 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 152 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 23.08 Time building geometry restraints manager: 22.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 16684 1.34 - 1.46: 6599 1.46 - 1.57: 28368 1.57 - 1.69: 161 1.69 - 1.81: 408 Bond restraints: 52220 Sorted by residual: bond pdb=" BE BEF c1002 " pdb=" F2 BEF c1002 " ideal model delta sigma weight residual 1.476 1.563 -0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" BE BEF f1002 " pdb=" F2 BEF f1002 " ideal model delta sigma weight residual 1.476 1.563 -0.087 2.00e-02 2.50e+03 1.87e+01 bond pdb=" BE BEF e1002 " pdb=" F2 BEF e1002 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" BE BEF d1002 " pdb=" F2 BEF d1002 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.83e+01 bond pdb=" BE BEF b 501 " pdb=" F2 BEF b 501 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.82e+01 ... (remaining 52215 not shown) Histogram of bond angle deviations from ideal: 99.36 - 106.73: 1826 106.73 - 114.09: 30526 114.09 - 121.45: 25492 121.45 - 128.82: 12731 128.82 - 136.18: 236 Bond angle restraints: 70811 Sorted by residual: angle pdb=" N ILE Y 500 " pdb=" CA ILE Y 500 " pdb=" C ILE Y 500 " ideal model delta sigma weight residual 111.91 108.02 3.89 8.90e-01 1.26e+00 1.91e+01 angle pdb=" F2 BEF f1002 " pdb=" BE BEF f1002 " pdb=" F3 BEF f1002 " ideal model delta sigma weight residual 119.96 107.30 12.66 3.00e+00 1.11e-01 1.78e+01 angle pdb=" C LEU A 183 " pdb=" N TYR A 184 " pdb=" CA TYR A 184 " ideal model delta sigma weight residual 122.58 113.86 8.72 2.07e+00 2.33e-01 1.78e+01 angle pdb=" F2 BEF b 501 " pdb=" BE BEF b 501 " pdb=" F3 BEF b 501 " ideal model delta sigma weight residual 119.96 107.33 12.63 3.00e+00 1.11e-01 1.77e+01 angle pdb=" F2 BEF c1002 " pdb=" BE BEF c1002 " pdb=" F3 BEF c1002 " ideal model delta sigma weight residual 119.96 107.37 12.59 3.00e+00 1.11e-01 1.76e+01 ... (remaining 70806 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.10: 30268 28.10 - 56.19: 1532 56.19 - 84.29: 151 84.29 - 112.38: 26 112.38 - 140.48: 5 Dihedral angle restraints: 31982 sinusoidal: 13781 harmonic: 18201 Sorted by residual: dihedral pdb=" C5' ADP e1000 " pdb=" O5' ADP e1000 " pdb=" PA ADP e1000 " pdb=" O2A ADP e1000 " ideal model delta sinusoidal sigma weight residual 300.00 164.30 135.70 1 2.00e+01 2.50e-03 4.12e+01 dihedral pdb=" O1B ADP c1000 " pdb=" O3A ADP c1000 " pdb=" PB ADP c1000 " pdb=" PA ADP c1000 " ideal model delta sinusoidal sigma weight residual 300.00 170.81 129.18 1 2.00e+01 2.50e-03 3.92e+01 dihedral pdb=" C5' ADP d1000 " pdb=" O5' ADP d1000 " pdb=" PA ADP d1000 " pdb=" O2A ADP d1000 " ideal model delta sinusoidal sigma weight residual 300.00 172.21 127.80 1 2.00e+01 2.50e-03 3.87e+01 ... (remaining 31979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 5846 0.039 - 0.078: 1555 0.078 - 0.117: 593 0.117 - 0.156: 90 0.156 - 0.195: 10 Chirality restraints: 8094 Sorted by residual: chirality pdb=" CB ILE e 382 " pdb=" CA ILE e 382 " pdb=" CG1 ILE e 382 " pdb=" CG2 ILE e 382 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.53e-01 chirality pdb=" CB ILE a 382 " pdb=" CA ILE a 382 " pdb=" CG1 ILE a 382 " pdb=" CG2 ILE a 382 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.49e-01 chirality pdb=" CB ILE c 382 " pdb=" CA ILE c 382 " pdb=" CG1 ILE c 382 " pdb=" CG2 ILE c 382 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.43e-01 ... (remaining 8091 not shown) Planarity restraints: 8994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS a 388 " 0.049 5.00e-02 4.00e+02 7.43e-02 8.84e+00 pdb=" N PRO a 389 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO a 389 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO a 389 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS f 388 " 0.049 5.00e-02 4.00e+02 7.43e-02 8.83e+00 pdb=" N PRO f 389 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO f 389 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO f 389 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS e 388 " -0.049 5.00e-02 4.00e+02 7.42e-02 8.82e+00 pdb=" N PRO e 389 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO e 389 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO e 389 " -0.041 5.00e-02 4.00e+02 ... (remaining 8991 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 769 2.60 - 3.18: 44856 3.18 - 3.75: 83143 3.75 - 4.33: 110408 4.33 - 4.90: 175770 Nonbonded interactions: 414946 Sorted by model distance: nonbonded pdb=" O2B ADP c1000 " pdb="MG MG c1001 " model vdw 2.026 2.170 nonbonded pdb=" O3' C R 99 " pdb="MG MG Y1501 " model vdw 2.056 2.170 nonbonded pdb="MG MG c1001 " pdb=" O HOH c1102 " model vdw 2.066 2.170 nonbonded pdb=" O2B ADP d1000 " pdb="MG MG d1001 " model vdw 2.074 2.170 nonbonded pdb=" O2B ADP e1000 " pdb="MG MG e1001 " model vdw 2.078 2.170 ... (remaining 414941 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'a' selection = (chain 'b' and resid 1 through 417) selection = (chain 'c' and resid 1 through 417) selection = (chain 'd' and resid 1 through 417) selection = (chain 'e' and resid 1 through 417) selection = (chain 'f' and resid 1 through 417) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians Zn 2 6.06 5 P 84 5.49 5 Mg 6 5.21 5 S 223 5.16 5 Be 5 3.05 5 C 31897 2.51 5 N 9072 2.21 5 O 10026 1.98 5 F 15 1.80 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 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: 0.040 Extract box with map and model: 10.610 Check model and map are aligned: 0.760 Convert atoms to be neutral: 0.430 Process input model: 145.070 Find NCS groups from input model: 2.500 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 164.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 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 : 0.003 0.087 52220 Z= 0.194 Angle : 0.650 12.656 70811 Z= 0.355 Chirality : 0.042 0.195 8094 Planarity : 0.004 0.074 8994 Dihedral : 15.587 140.477 20234 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer Outliers : 4.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.10 % 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: -3.41 (0.09), residues: 6307 helix: -1.70 (0.09), residues: 2376 sheet: -1.78 (0.15), residues: 912 loop : -2.90 (0.09), residues: 3019 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 429 time to evaluate : 6.913 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 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 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 264 outliers final: 54 residues processed: 649 average time/residue: 0.6687 time to fit residues: 712.0905 Evaluate side-chains 333 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 279 time to evaluate : 5.965 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 54 outliers final: 1 residues processed: 54 average time/residue: 0.5021 time to fit residues: 57.5916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 533 optimal weight: 0.8980 chunk 479 optimal weight: 7.9990 chunk 265 optimal weight: 30.0000 chunk 163 optimal weight: 1.9990 chunk 323 optimal weight: 1.9990 chunk 255 optimal weight: 8.9990 chunk 495 optimal weight: 20.0000 chunk 191 optimal weight: 7.9990 chunk 301 optimal weight: 20.0000 chunk 368 optimal weight: 1.9990 chunk 573 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 32 GLN ** a 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 198 ASN a 295 HIS a 388 HIS b 32 GLN ** b 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 198 ASN b 295 HIS b 388 HIS c 32 GLN ** c 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 198 ASN c 295 HIS d 32 GLN d 90 ASN d 198 ASN ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 140 HIS e 198 ASN ** e 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 388 HIS ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 198 ASN f 295 HIS ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 GLN A 129 GLN A 157 ASN A 303 HIS A 321 ASN A 324 ASN A 412 ASN U 103 ASN U 160 HIS U 227 GLN W 29 GLN X 139 ASN ** X 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 684 ASN X 688 GLN ** X 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 932 GLN X1116 HIS ** X1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 157 GLN Y 365 GLN Y 477 GLN Y 739 GLN Y1049 GLN ** Y1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 52220 Z= 0.175 Angle : 0.564 9.207 70811 Z= 0.282 Chirality : 0.041 0.192 8094 Planarity : 0.005 0.114 8994 Dihedral : 10.372 144.368 7721 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.10 % 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: -2.39 (0.10), residues: 6307 helix: -0.68 (0.10), residues: 2369 sheet: -1.39 (0.16), residues: 899 loop : -2.40 (0.10), residues: 3039 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 322 time to evaluate : 6.055 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 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 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: 4 outliers final: 1 residues processed: 326 average time/residue: 0.7097 time to fit residues: 381.9905 Evaluate side-chains 260 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 259 time to evaluate : 5.986 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5141 time to fit residues: 9.1340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 318 optimal weight: 8.9990 chunk 178 optimal weight: 20.0000 chunk 477 optimal weight: 8.9990 chunk 390 optimal weight: 5.9990 chunk 158 optimal weight: 8.9990 chunk 574 optimal weight: 7.9990 chunk 621 optimal weight: 8.9990 chunk 512 optimal weight: 0.9990 chunk 570 optimal weight: 6.9990 chunk 196 optimal weight: 6.9990 chunk 461 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 42 HIS a 90 ASN a 295 HIS ** a 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 HIS b 140 HIS b 295 HIS ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 42 HIS c 388 HIS d 140 HIS e 90 ASN ** e 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 132 HIS U 160 HIS X 41 GLN X 46 GLN ** X 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 330 HIS ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 799 ASN X 808 ASN X 832 HIS ** X1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X1157 GLN Y 196 GLN Y 817 HIS Y1259 GLN ** Y1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 52220 Z= 0.289 Angle : 0.678 9.823 70811 Z= 0.343 Chirality : 0.042 0.292 8094 Planarity : 0.005 0.128 8994 Dihedral : 10.554 150.161 7721 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 23.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.10 % 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: -1.73 (0.10), residues: 6307 helix: -0.06 (0.11), residues: 2327 sheet: -1.18 (0.16), residues: 928 loop : -2.01 (0.10), residues: 3052 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 285 time to evaluate : 6.468 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 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 revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 292 average time/residue: 0.6602 time to fit residues: 323.9593 Evaluate side-chains 240 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 238 time to evaluate : 5.813 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4193 time to fit residues: 9.5271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 568 optimal weight: 20.0000 chunk 432 optimal weight: 20.0000 chunk 298 optimal weight: 4.9990 chunk 63 optimal weight: 20.0000 chunk 274 optimal weight: 8.9990 chunk 386 optimal weight: 30.0000 chunk 577 optimal weight: 2.9990 chunk 610 optimal weight: 9.9990 chunk 301 optimal weight: 20.0000 chunk 546 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 90 ASN ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 344 HIS ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 140 HIS ** c 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 344 HIS d 388 HIS ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 344 HIS f 344 HIS U 160 HIS ** W 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 31 GLN ** X 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 832 HIS ** X1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X1209 GLN ** X1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1307 ASN Y 232 ASN Y 277 ASN ** Y 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 450 HIS Y1197 ASN ** Y1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.123 52220 Z= 0.329 Angle : 0.696 14.555 70811 Z= 0.355 Chirality : 0.042 0.187 8094 Planarity : 0.005 0.124 8994 Dihedral : 10.731 155.012 7721 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 28.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.10 % 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: -1.59 (0.10), residues: 6307 helix: -0.12 (0.10), residues: 2384 sheet: -1.09 (0.17), residues: 879 loop : -1.80 (0.11), residues: 3044 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 259 time to evaluate : 6.139 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 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: 2 outliers final: 1 residues processed: 261 average time/residue: 0.6566 time to fit residues: 291.0309 Evaluate side-chains 228 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 227 time to evaluate : 6.030 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4581 time to fit residues: 9.0989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 508 optimal weight: 4.9990 chunk 346 optimal weight: 9.9990 chunk 8 optimal weight: 20.0000 chunk 454 optimal weight: 0.8980 chunk 252 optimal weight: 9.9990 chunk 521 optimal weight: 0.5980 chunk 422 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 311 optimal weight: 3.9990 chunk 548 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 32 GLN ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 32 GLN ** c 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 189 GLN ** V 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X1157 GLN X1314 GLN Y 277 ASN ** Y 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1197 ASN Y1295 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 52220 Z= 0.179 Angle : 0.578 10.269 70811 Z= 0.289 Chirality : 0.041 0.198 8094 Planarity : 0.004 0.066 8994 Dihedral : 10.601 152.076 7721 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.10 % 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: -1.26 (0.10), residues: 6307 helix: 0.18 (0.11), residues: 2369 sheet: -1.09 (0.16), residues: 939 loop : -1.56 (0.11), residues: 2999 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 5.887 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 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: 0 outliers final: 0 residues processed: 272 average time/residue: 0.6741 time to fit residues: 306.9975 Evaluate side-chains 237 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 6.061 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.1675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 205 optimal weight: 20.0000 chunk 550 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 358 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 611 optimal weight: 10.0000 chunk 507 optimal weight: 20.0000 chunk 283 optimal weight: 40.0000 chunk 50 optimal weight: 30.0000 chunk 202 optimal weight: 10.0000 chunk 321 optimal weight: 30.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 344 HIS ** d 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 90 ASN ** e 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 14 ASN U 160 HIS U 227 GLN ** W 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 36 GLN ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 277 ASN ** Y 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1108 GLN Y1197 ASN Y1279 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.5336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.100 52220 Z= 0.378 Angle : 0.783 13.673 70811 Z= 0.397 Chirality : 0.044 0.275 8094 Planarity : 0.006 0.148 8994 Dihedral : 10.918 147.818 7721 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 36.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.10 % 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: -1.46 (0.10), residues: 6307 helix: -0.16 (0.10), residues: 2396 sheet: -1.12 (0.17), residues: 897 loop : -1.55 (0.11), residues: 3014 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 250 time to evaluate : 6.418 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 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: 1 outliers final: 1 residues processed: 251 average time/residue: 0.6706 time to fit residues: 287.8639 Evaluate side-chains 222 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 221 time to evaluate : 6.176 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4476 time to fit residues: 8.9992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 589 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 348 optimal weight: 5.9990 chunk 446 optimal weight: 20.0000 chunk 345 optimal weight: 6.9990 chunk 514 optimal weight: 0.0060 chunk 341 optimal weight: 9.9990 chunk 609 optimal weight: 0.9980 chunk 381 optimal weight: 8.9990 chunk 371 optimal weight: 1.9990 chunk 281 optimal weight: 30.0000 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 90 ASN ** c 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 126 ASN e 135 ASN ** f 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 14 ASN ** V 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 194 GLN ** W 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 277 ASN ** Y 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1197 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 52220 Z= 0.175 Angle : 0.596 10.619 70811 Z= 0.298 Chirality : 0.042 0.227 8094 Planarity : 0.004 0.061 8994 Dihedral : 10.688 148.026 7721 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.10 % 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: -1.12 (0.10), residues: 6307 helix: 0.24 (0.11), residues: 2363 sheet: -1.11 (0.16), residues: 933 loop : -1.38 (0.11), residues: 3011 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 259 time to evaluate : 6.690 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 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: 1 outliers final: 0 residues processed: 260 average time/residue: 0.6883 time to fit residues: 303.9630 Evaluate side-chains 227 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 5.757 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.6374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 376 optimal weight: 8.9990 chunk 243 optimal weight: 5.9990 chunk 363 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 387 optimal weight: 4.9990 chunk 415 optimal weight: 10.0000 chunk 301 optimal weight: 8.9990 chunk 56 optimal weight: 20.0000 chunk 478 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 14 ASN A 260 GLN ** W 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 31 GLN X 357 ASN ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 277 ASN ** Y 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.5750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 52220 Z= 0.329 Angle : 0.708 12.691 70811 Z= 0.359 Chirality : 0.042 0.243 8094 Planarity : 0.005 0.059 8994 Dihedral : 10.824 146.935 7721 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 32.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.10 % 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: -1.21 (0.10), residues: 6307 helix: 0.08 (0.11), residues: 2367 sheet: -1.09 (0.17), residues: 899 loop : -1.39 (0.11), residues: 3041 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 6.189 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.6627 time to fit residues: 276.7868 Evaluate side-chains 213 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 6.079 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.1026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 554 optimal weight: 1.9990 chunk 583 optimal weight: 9.9990 chunk 532 optimal weight: 0.0470 chunk 567 optimal weight: 0.8980 chunk 341 optimal weight: 10.0000 chunk 247 optimal weight: 40.0000 chunk 445 optimal weight: 0.0370 chunk 174 optimal weight: 0.2980 chunk 512 optimal weight: 5.9990 chunk 536 optimal weight: 8.9990 chunk 565 optimal weight: 6.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 126 ASN ** f 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 189 GLN A 14 ASN V 23 HIS V 194 GLN ** W 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X1236 ASN Y 277 ASN ** Y 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.5516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 52220 Z= 0.168 Angle : 0.603 11.079 70811 Z= 0.299 Chirality : 0.042 0.218 8094 Planarity : 0.004 0.060 8994 Dihedral : 10.655 148.947 7721 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.10 % 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: -1.03 (0.10), residues: 6307 helix: 0.28 (0.11), residues: 2375 sheet: -1.11 (0.17), residues: 924 loop : -1.29 (0.11), residues: 3008 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 6.053 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 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: 0 outliers final: 0 residues processed: 248 average time/residue: 0.6577 time to fit residues: 278.6472 Evaluate side-chains 224 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 6.223 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.7577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 372 optimal weight: 0.0570 chunk 600 optimal weight: 8.9990 chunk 366 optimal weight: 0.0470 chunk 284 optimal weight: 10.0000 chunk 417 optimal weight: 5.9990 chunk 629 optimal weight: 10.0000 chunk 579 optimal weight: 20.0000 chunk 501 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 387 optimal weight: 10.0000 chunk 307 optimal weight: 1.9990 overall best weight: 3.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 126 ASN ** f 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 613 ASN ** X 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.5703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 52220 Z= 0.200 Angle : 0.600 14.132 70811 Z= 0.300 Chirality : 0.041 0.221 8094 Planarity : 0.004 0.054 8994 Dihedral : 10.616 148.011 7721 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 23.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.10 % 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: -0.92 (0.11), residues: 6307 helix: 0.39 (0.11), residues: 2380 sheet: -1.08 (0.17), residues: 926 loop : -1.23 (0.11), residues: 3001 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 6.301 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 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: 0 outliers final: 0 residues processed: 243 average time/residue: 0.6411 time to fit residues: 268.3657 Evaluate side-chains 221 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 6.238 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.2223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 398 optimal weight: 20.0000 chunk 534 optimal weight: 20.0000 chunk 153 optimal weight: 1.9990 chunk 462 optimal weight: 8.9990 chunk 74 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 chunk 502 optimal weight: 1.9990 chunk 210 optimal weight: 20.0000 chunk 515 optimal weight: 50.0000 chunk 63 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X1307 ASN Y 277 ASN ** Y 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.035598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.021374 restraints weight = 803075.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.021744 restraints weight = 566960.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.022163 restraints weight = 442389.504| |-----------------------------------------------------------------------------| r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.6129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 52220 Z= 0.252 Angle : 0.642 10.999 70811 Z= 0.324 Chirality : 0.042 0.239 8094 Planarity : 0.004 0.068 8994 Dihedral : 10.713 148.507 7721 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 27.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.11), residues: 6307 helix: 0.34 (0.11), residues: 2373 sheet: -1.02 (0.17), residues: 895 loop : -1.25 (0.11), residues: 3039 =============================================================================== Job complete usr+sys time: 8457.71 seconds wall clock time: 156 minutes 21.05 seconds (9381.05 seconds total)