Starting phenix.real_space_refine (version: dev) on Thu Dec 22 21:31:06 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ade_11725/12_2022/7ade_11725_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ade_11725/12_2022/7ade_11725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ade_11725/12_2022/7ade_11725.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ade_11725/12_2022/7ade_11725.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ade_11725/12_2022/7ade_11725_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ade_11725/12_2022/7ade_11725_updated.pdb" } resolution = 4.2 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= 0.003 sd= 0.018 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 "f ARG 30": "NH1" <-> "NH2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "f GLU 118": "OE1" <-> "OE2" Residue "f ARG 299": "NH1" <-> "NH2" Residue "f GLU 333": "OE1" <-> "OE2" Residue "f GLU 342": "OE1" <-> "OE2" Residue "f ARG 347": "NH1" <-> "NH2" Residue "f ARG 366": "NH1" <-> "NH2" Residue "f ARG 384": "NH1" <-> "NH2" Residue "f GLU 414": "OE1" <-> "OE2" Residue "a ARG 30": "NH1" <-> "NH2" Residue "a ARG 92": "NH1" <-> "NH2" Residue "a GLU 118": "OE1" <-> "OE2" Residue "a ARG 299": "NH1" <-> "NH2" Residue "a GLU 333": "OE1" <-> "OE2" Residue "a GLU 342": "OE1" <-> "OE2" Residue "a ARG 347": "NH1" <-> "NH2" Residue "a ARG 366": "NH1" <-> "NH2" Residue "a ARG 384": "NH1" <-> "NH2" Residue "a GLU 414": "OE1" <-> "OE2" Residue "b ARG 30": "NH1" <-> "NH2" Residue "b ARG 92": "NH1" <-> "NH2" Residue "b GLU 118": "OE1" <-> "OE2" Residue "b ARG 299": "NH1" <-> "NH2" Residue "b GLU 333": "OE1" <-> "OE2" Residue "b GLU 342": "OE1" <-> "OE2" Residue "b ARG 347": "NH1" <-> "NH2" Residue "b ARG 366": "NH1" <-> "NH2" Residue "b ARG 384": "NH1" <-> "NH2" Residue "b GLU 414": "OE1" <-> "OE2" Residue "c ARG 30": "NH1" <-> "NH2" Residue "c ARG 92": "NH1" <-> "NH2" Residue "c GLU 118": "OE1" <-> "OE2" Residue "c ARG 299": "NH1" <-> "NH2" Residue "c GLU 333": "OE1" <-> "OE2" Residue "c GLU 342": "OE1" <-> "OE2" Residue "c ARG 347": "NH1" <-> "NH2" Residue "c ARG 366": "NH1" <-> "NH2" Residue "c ARG 384": "NH1" <-> "NH2" Residue "c GLU 414": "OE1" <-> "OE2" Residue "d ARG 30": "NH1" <-> "NH2" Residue "d ARG 92": "NH1" <-> "NH2" Residue "d GLU 118": "OE1" <-> "OE2" Residue "d ARG 299": "NH1" <-> "NH2" Residue "d GLU 333": "OE1" <-> "OE2" Residue "d GLU 342": "OE1" <-> "OE2" Residue "d ARG 347": "NH1" <-> "NH2" Residue "d ARG 366": "NH1" <-> "NH2" Residue "d ARG 384": "NH1" <-> "NH2" Residue "d GLU 414": "OE1" <-> "OE2" Residue "e ARG 30": "NH1" <-> "NH2" Residue "e ARG 92": "NH1" <-> "NH2" Residue "e GLU 118": "OE1" <-> "OE2" Residue "e ARG 299": "NH1" <-> "NH2" Residue "e GLU 333": "OE1" <-> "OE2" Residue "e GLU 342": "OE1" <-> "OE2" Residue "e ARG 347": "NH1" <-> "NH2" Residue "e ARG 366": "NH1" <-> "NH2" Residue "e ARG 384": "NH1" <-> "NH2" Residue "e GLU 414": "OE1" <-> "OE2" Residue "A GLU 78": "OE1" <-> "OE2" Residue "A ARG 123": "NH1" <-> "NH2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A ARG 320": "NH1" <-> "NH2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A GLU 376": "OE1" <-> "OE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A GLU 494": "OE1" <-> "OE2" Residue "U ARG 33": "NH1" <-> "NH2" Residue "U ARG 219": "NH1" <-> "NH2" Residue "V ARG 12": "NH1" <-> "NH2" Residue "V GLU 29": "OE1" <-> "OE2" Residue "V ARG 33": "NH1" <-> "NH2" Residue "V TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 163": "OE1" <-> "OE2" Residue "V GLU 181": "OE1" <-> "OE2" Residue "V ARG 265": "NH1" <-> "NH2" Residue "V GLU 288": "OE1" <-> "OE2" Residue "W GLU 11": "OE1" <-> "OE2" Residue "W GLU 56": "OE1" <-> "OE2" Residue "W GLU 74": "OE1" <-> "OE2" Residue "W GLU 76": "OE1" <-> "OE2" Residue "X ARG 10": "NH1" <-> "NH2" Residue "X GLU 77": "OE1" <-> "OE2" Residue "X GLU 111": "OE1" <-> "OE2" Residue "X GLU 119": "OE1" <-> "OE2" Residue "X ARG 151": "NH1" <-> "NH2" Residue "X ARG 180": "NH1" <-> "NH2" Residue "X GLU 218": "OE1" <-> "OE2" Residue "X ARG 268": "NH1" <-> "NH2" Residue "X ARG 371": "NH1" <-> "NH2" Residue "X GLU 441": "OE1" <-> "OE2" Residue "X ARG 451": "NH1" <-> "NH2" Residue "X GLU 565": "OE1" <-> "OE2" Residue "X GLU 611": "OE1" <-> "OE2" Residue "X ARG 647": "NH1" <-> "NH2" Residue "X GLU 813": "OE1" <-> "OE2" Residue "X GLU 849": "OE1" <-> "OE2" Residue "X ARG 903": "NH1" <-> "NH2" Residue "X ARG 996": "NH1" <-> "NH2" Residue "X ARG 1034": "NH1" <-> "NH2" Residue "X ARG 1106": "NH1" <-> "NH2" Residue "X ARG 1171": "NH1" <-> "NH2" Residue "X GLU 1174": "OE1" <-> "OE2" Residue "Y GLU 37": "OE1" <-> "OE2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 53": "NH1" <-> "NH2" Residue "Y ARG 101": "NH1" <-> "NH2" Residue "Y ARG 123": "NH1" <-> "NH2" Residue "Y ARG 133": "NH1" <-> "NH2" Residue "Y GLU 155": "OE1" <-> "OE2" Residue "Y TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 271": "NH1" <-> "NH2" Residue "Y ARG 281": "NH1" <-> "NH2" Residue "Y ARG 339": "NH1" <-> "NH2" Residue "Y GLU 375": "OE1" <-> "OE2" Residue "Y GLU 386": "OE1" <-> "OE2" Residue "Y GLU 414": "OE1" <-> "OE2" Residue "Y ARG 425": "NH1" <-> "NH2" Residue "Y GLU 497": "OE1" <-> "OE2" Residue "Y ARG 515": "NH1" <-> "NH2" Residue "Y ARG 634": "NH1" <-> "NH2" Residue "Y ARG 692": "NH1" <-> "NH2" Residue "Y GLU 714": "OE1" <-> "OE2" Residue "Y GLU 765": "OE1" <-> "OE2" Residue "Y GLU 827": "OE1" <-> "OE2" Residue "Y ARG 836": "NH1" <-> "NH2" Residue "Y GLU 913": "OE1" <-> "OE2" Residue "Y ARG 933": "NH1" <-> "NH2" Residue "Y ARG 943": "NH1" <-> "NH2" Residue "Y ARG 1036": "NH1" <-> "NH2" Residue "Y GLU 1066": "OE1" <-> "OE2" Residue "Y GLU 1146": "OE1" <-> "OE2" Residue "Y ARG 1148": "NH1" <-> "NH2" Residue "Y GLU 1187": "OE1" <-> "OE2" Residue "Y GLU 1188": "OE1" <-> "OE2" Residue "Y GLU 1215": "OE1" <-> "OE2" Residue "Y ARG 1258": "NH1" <-> "NH2" Residue "Y GLU 1327": "OE1" <-> "OE2" Residue "Y ARG 1345": "NH1" <-> "NH2" Residue "Y ARG 1373": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 51553 Number of models: 1 Model: "" Number of chains: 26 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: 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: "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: 1825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1825 Classifications: {'peptide': 235} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 225} Chain: "V" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2504 Classifications: {'peptide': 321} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 303} 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: 10431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1343, 10431 Classifications: {'peptide': 1343} Link IDs: {'PTRANS': 54, 'TRANS': 1288} Chain breaks: 1 Chain: "L" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 741 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 474 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 674 Classifications: {'RNA': 32} Modifications used: {'rna2p_pyr': 4, 'rna3p_pur': 14, 'rna3p_pyr': 14} Link IDs: {'rna2p': 4, 'rna3p': 27} Chain breaks: 1 Chain: "a" 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: "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: "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: "a" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 39504 SG CYS Y 70 57.251 119.873 115.660 1.00255.29 S ATOM 39518 SG CYS Y 72 57.104 116.504 116.477 1.00254.09 S ATOM 39626 SG CYS Y 85 55.146 118.411 118.894 1.00259.98 S ATOM 45224 SG CYS Y 814 72.424 185.924 117.303 1.00120.89 S ATOM 45789 SG CYS Y 888 74.512 181.871 117.403 1.00111.12 S ATOM 45840 SG CYS Y 895 71.574 181.911 115.497 1.00113.71 S ATOM 45861 SG CYS Y 898 75.032 184.652 115.284 1.00 98.22 S Time building chain proxies: 27.63, per 1000 atoms: 0.54 Number of scatterers: 51553 At special positions: 0 Unit cell: (163.68, 228.16, 192.2, 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 102 15.00 Mg 6 11.99 F 15 9.00 O 10112 8.00 N 9103 7.00 C 31985 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=0, symmetry=0 Time building additional restraints: 20.83 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 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 : 6 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11722 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 223 helices and 43 sheets defined 34.9% alpha, 10.9% beta 21 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 16.68 Creating SS restraints... 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 31 through 44 Processing helix chain 'f' and resid 83 through 88 Processing helix chain 'f' and resid 124 through 128 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 219 Processing helix chain 'f' and resid 236 through 255 Processing helix chain 'f' and resid 267 through 277 Processing helix chain 'f' and resid 292 through 302 removed outlier: 4.567A 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 334 Processing helix chain 'f' and resid 347 through 350 No H-bonds generated for 'chain 'f' and resid 347 through 350' Processing helix chain 'f' and resid 368 through 370 No H-bonds generated for 'chain 'f' and resid 368 through 370' Processing helix chain 'f' and resid 374 through 388 Processing helix chain 'f' and resid 393 through 405 removed outlier: 4.026A pdb=" N MET f 405 " --> pdb=" O ASN f 401 " (cutoff:3.500A) Processing helix chain 'f' and resid 409 through 416 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 31 through 44 Processing helix chain 'a' and resid 83 through 88 Processing helix chain 'a' and resid 124 through 128 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 219 Processing helix chain 'a' and resid 236 through 255 Processing helix chain 'a' and resid 267 through 277 Processing helix chain 'a' and resid 292 through 302 removed outlier: 4.566A 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 334 Processing helix chain 'a' and resid 347 through 350 No H-bonds generated for 'chain 'a' and resid 347 through 350' Processing helix chain 'a' and resid 368 through 370 No H-bonds generated for 'chain 'a' and resid 368 through 370' Processing helix chain 'a' and resid 374 through 388 Processing helix chain 'a' and resid 393 through 405 removed outlier: 4.025A pdb=" N MET a 405 " --> pdb=" O ASN a 401 " (cutoff:3.500A) 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 31 through 44 Processing helix chain 'b' and resid 83 through 88 Processing helix chain 'b' and resid 124 through 128 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 219 Processing helix chain 'b' and resid 236 through 255 Processing helix chain 'b' and resid 267 through 277 Processing helix chain 'b' and resid 292 through 302 removed outlier: 4.567A 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 334 Processing helix chain 'b' and resid 347 through 350 No H-bonds generated for 'chain 'b' and resid 347 through 350' Processing helix chain 'b' and resid 368 through 370 No H-bonds generated for 'chain 'b' and resid 368 through 370' Processing helix chain 'b' and resid 374 through 388 Processing helix chain 'b' and resid 393 through 405 removed outlier: 4.026A pdb=" N MET b 405 " --> pdb=" O ASN b 401 " (cutoff:3.500A) 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 31 through 44 Processing helix chain 'c' and resid 83 through 88 Processing helix chain 'c' and resid 124 through 128 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 219 Processing helix chain 'c' and resid 236 through 255 Processing helix chain 'c' and resid 267 through 277 Processing helix chain 'c' and resid 292 through 302 removed outlier: 4.567A 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 334 Processing helix chain 'c' and resid 347 through 350 No H-bonds generated for 'chain 'c' and resid 347 through 350' Processing helix chain 'c' and resid 368 through 370 No H-bonds generated for 'chain 'c' and resid 368 through 370' Processing helix chain 'c' and resid 374 through 388 Processing helix chain 'c' and resid 393 through 405 removed outlier: 4.026A pdb=" N MET c 405 " --> pdb=" O ASN c 401 " (cutoff:3.500A) 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 31 through 44 Processing helix chain 'd' and resid 83 through 88 Processing helix chain 'd' and resid 124 through 128 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 219 Processing helix chain 'd' and resid 236 through 255 Processing helix chain 'd' and resid 267 through 277 Processing helix chain 'd' and resid 292 through 302 removed outlier: 4.566A 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 334 Processing helix chain 'd' and resid 347 through 350 No H-bonds generated for 'chain 'd' and resid 347 through 350' Processing helix chain 'd' and resid 368 through 370 No H-bonds generated for 'chain 'd' and resid 368 through 370' Processing helix chain 'd' and resid 374 through 388 Processing helix chain 'd' and resid 393 through 405 removed outlier: 4.026A pdb=" N MET d 405 " --> pdb=" O ASN d 401 " (cutoff:3.500A) 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 31 through 44 Processing helix chain 'e' and resid 83 through 88 Processing helix chain 'e' and resid 124 through 128 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 219 Processing helix chain 'e' and resid 236 through 255 Processing helix chain 'e' and resid 267 through 277 Processing helix chain 'e' and resid 292 through 302 removed outlier: 4.566A 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 334 Processing helix chain 'e' and resid 347 through 350 No H-bonds generated for 'chain 'e' and resid 347 through 350' Processing helix chain 'e' and resid 368 through 370 No H-bonds generated for 'chain 'e' and resid 368 through 370' Processing helix chain 'e' and resid 374 through 388 Processing helix chain 'e' and resid 393 through 405 removed outlier: 4.026A pdb=" N MET e 405 " --> pdb=" O ASN e 401 " (cutoff:3.500A) Processing helix chain 'e' and resid 409 through 416 Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 20 through 38 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 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' 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 130 Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'A' and resid 259 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 323 through 331 removed outlier: 4.488A pdb=" N ALA A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 400 through 425 Processing helix chain 'A' and resid 442 through 450 Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' 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 156 through 158 No H-bonds generated for 'chain 'U' and resid 156 through 158' Processing helix chain 'U' and resid 213 through 229 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 87 removed outlier: 3.687A pdb=" N GLY V 87 " --> pdb=" O LEU V 83 " (cutoff:3.500A) 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 156 through 164 removed outlier: 3.835A pdb=" N HIS V 160 " --> pdb=" O SER V 156 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER V 161 " --> pdb=" O THR V 157 " (cutoff:3.500A) Processing helix chain 'V' and resid 213 through 231 removed outlier: 4.792A pdb=" N ALA V 230 " --> pdb=" O GLU V 226 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N PHE V 231 " --> pdb=" O GLN V 227 " (cutoff:3.500A) Processing helix chain 'V' and resid 257 through 260 Processing helix chain 'V' and resid 264 through 273 removed outlier: 3.842A pdb=" N GLU V 273 " --> pdb=" O CYS V 269 " (cutoff:3.500A) Processing helix chain 'V' and resid 279 through 282 No H-bonds generated for 'chain 'V' and resid 279 through 282' Processing helix chain 'V' and resid 297 through 309 Processing helix chain 'W' and resid 7 through 12 Processing helix chain 'W' and resid 16 through 30 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 43 through 45 No H-bonds generated for 'chain 'X' and resid 43 through 45' Processing helix chain 'X' and resid 49 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: 3.918A pdb=" N LEU X 213 " --> pdb=" O ILE X 209 " (cutoff:3.500A) Processing helix chain 'X' and resid 217 through 224 Processing helix chain 'X' and resid 271 through 280 Processing helix chain 'X' and resid 289 through 293 Processing helix chain 'X' and resid 319 through 327 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 436 Processing helix chain 'X' and resid 456 through 479 Processing helix chain 'X' and resid 495 through 507 removed outlier: 3.547A pdb=" N PHE X 505 " --> pdb=" O ALA X 501 " (cutoff:3.500A) 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 610 through 612 No H-bonds generated for 'chain 'X' and resid 610 through 612' Processing helix chain 'X' and resid 676 through 687 removed outlier: 3.660A pdb=" N ASN X 684 " --> pdb=" O LEU X 680 " (cutoff:3.500A) Processing helix chain 'X' and resid 704 through 711 Processing helix chain 'X' and resid 820 through 825 Processing helix chain 'X' and resid 859 through 864 removed outlier: 4.508A pdb=" N LYS X 864 " --> pdb=" O ALA X 860 " (cutoff:3.500A) Processing helix chain 'X' and resid 897 through 903 Processing helix chain 'X' and resid 943 through 978 Processing helix chain 'X' and resid 980 through 989 removed outlier: 5.535A pdb=" N VAL X 984 " --> pdb=" O ALA X 981 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU X 985 " --> pdb=" O GLY X 982 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU X 989 " --> pdb=" O ALA X 986 " (cutoff:3.500A) Processing helix chain 'X' and resid 993 through 995 No H-bonds generated for 'chain 'X' and resid 993 through 995' Processing helix chain 'X' and resid 1004 through 1037 removed outlier: 4.860A pdb=" N ASN X1009 " --> pdb=" O GLU X1005 " (cutoff:3.500A) Processing helix chain 'X' and resid 1102 through 1106 removed outlier: 3.527A pdb=" N ARG X1106 " --> pdb=" O GLY X1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 1102 through 1106' 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 1176 Processing helix chain 'X' and resid 1192 through 1201 Processing helix chain 'X' and resid 1261 through 1263 No H-bonds generated for 'chain 'X' and resid 1261 through 1263' 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 removed outlier: 3.818A pdb=" N THR X1302 " --> pdb=" O VAL X1298 " (cutoff:3.500A) Processing helix chain 'X' and resid 1321 through 1333 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 123 through 128 Processing helix chain 'Y' and resid 132 through 139 Processing helix chain 'Y' and resid 162 through 166 Processing helix chain 'Y' and resid 181 through 190 Processing helix chain 'Y' and resid 196 through 207 Processing helix chain 'Y' and resid 212 through 229 Processing helix chain 'Y' and resid 235 through 237 No H-bonds generated for 'chain 'Y' and resid 235 through 237' Processing helix chain 'Y' and resid 247 through 250 Processing helix chain 'Y' and resid 265 through 284 Processing helix chain 'Y' and resid 290 through 307 removed outlier: 4.379A pdb=" N LEU Y 299 " --> pdb=" O GLU Y 295 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP Y 304 " --> pdb=" O GLN Y 300 " (cutoff:3.500A) Processing helix chain 'Y' and resid 327 through 333 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 409 through 415 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 453 through 457 Processing helix chain 'Y' and resid 474 through 482 Processing helix chain 'Y' and resid 504 through 514 Processing helix chain 'Y' and resid 530 through 538 Processing helix chain 'Y' and resid 574 through 581 removed outlier: 4.024A pdb=" N MET Y 581 " --> pdb=" O ALA Y 577 " (cutoff:3.500A) Processing helix chain 'Y' and resid 598 through 612 Processing helix chain 'Y' and resid 615 through 635 removed outlier: 4.445A pdb=" N ILE Y 619 " --> pdb=" O LYS Y 615 " (cutoff:3.500A) Processing helix chain 'Y' and resid 650 through 670 Processing helix chain 'Y' and resid 675 through 701 removed outlier: 3.836A pdb=" N ASP Y 684 " --> pdb=" O ASN Y 680 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE Y 685 " --> pdb=" O LYS Y 681 " (cutoff:3.500A) Processing helix chain 'Y' and resid 721 through 727 Processing helix chain 'Y' and resid 734 through 741 Processing helix chain 'Y' and resid 769 through 803 removed outlier: 3.996A pdb=" N LYS Y 781 " --> pdb=" O HIS Y 777 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY Y 782 " --> pdb=" O GLY Y 778 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR Y 786 " --> pdb=" O GLY Y 782 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA Y 787 " --> pdb=" O LEU Y 783 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA Y 791 " --> pdb=" O ALA Y 787 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASN Y 792 " --> pdb=" O LEU Y 788 " (cutoff:3.500A) Processing helix chain 'Y' and resid 836 through 839 No H-bonds generated for 'chain 'Y' and resid 836 through 839' Processing helix chain 'Y' and resid 866 through 874 Processing helix chain 'Y' and resid 915 through 929 Proline residue: Y 926 - end of helix removed outlier: 4.958A pdb=" N GLN Y 929 " --> pdb=" O GLU Y 925 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1069 through 1072 No H-bonds generated for 'chain 'Y' and resid 1069 through 1072' Processing helix chain 'Y' and resid 1138 through 1146 Processing helix chain 'Y' and resid 1217 through 1224 Processing helix chain 'Y' and resid 1227 through 1244 removed outlier: 3.702A pdb=" N GLN Y1244 " --> pdb=" O VAL Y1240 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1250 through 1260 Processing helix chain 'Y' and resid 1282 through 1294 removed outlier: 4.161A pdb=" N GLU Y1291 " --> pdb=" O ILE Y1287 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU Y1292 " --> pdb=" O ALA Y1288 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA Y1294 " --> pdb=" O ARG Y1290 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1309 through 1314 removed outlier: 3.572A pdb=" N LEU Y1314 " --> pdb=" O THR Y1310 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1319 through 1322 No H-bonds generated for 'chain 'Y' and resid 1319 through 1322' Processing helix chain 'Y' and resid 1328 through 1338 Processing helix chain 'Y' and resid 1348 through 1351 No H-bonds generated for 'chain 'Y' and resid 1348 through 1351' Processing helix chain 'Y' and resid 1361 through 1372 removed outlier: 3.626A pdb=" N TYR Y1365 " --> pdb=" O THR Y1361 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'f' and resid 79 through 81 removed outlier: 5.950A pdb=" N LYS f 100 " --> pdb=" O VAL f 116 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N VAL f 116 " --> pdb=" O LYS f 100 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'f' and resid 341 through 345 removed outlier: 8.515A pdb=" N GLY f 174 " --> pdb=" O LEU f 313 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE f 315 " --> pdb=" O GLY f 174 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ILE f 176 " --> pdb=" O ILE f 315 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ALA f 317 " --> pdb=" O ILE f 176 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ALA f 178 " --> pdb=" O ALA f 317 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ALA f 319 " --> pdb=" O ALA f 178 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL f 260 " --> pdb=" O THR f 314 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE f 316 " --> pdb=" O VAL f 260 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE f 262 " --> pdb=" O ILE f 316 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N THR f 318 " --> pdb=" O ILE f 262 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU f 264 " --> pdb=" O THR f 318 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N LEU f 320 " --> pdb=" O LEU f 264 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL f 203 " --> pdb=" O ILE f 261 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N LEU f 263 " --> pdb=" O VAL f 203 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N MET f 205 " --> pdb=" O LEU f 263 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N ASP f 265 " --> pdb=" O MET f 205 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU f 207 " --> pdb=" O ASP f 265 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL f 228 " --> pdb=" O VAL f 206 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU f 208 " --> pdb=" O VAL f 228 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'a' and resid 79 through 81 removed outlier: 5.949A pdb=" N LYS a 100 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N VAL a 116 " --> pdb=" O LYS a 100 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'a' and resid 341 through 345 removed outlier: 8.514A pdb=" N GLY a 174 " --> pdb=" O LEU a 313 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE a 315 " --> pdb=" O GLY a 174 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ILE a 176 " --> pdb=" O ILE a 315 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ALA a 317 " --> pdb=" O ILE a 176 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N ALA a 178 " --> pdb=" O ALA a 317 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA a 319 " --> pdb=" O ALA a 178 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL a 260 " --> pdb=" O THR a 314 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ILE a 316 " --> pdb=" O VAL a 260 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE a 262 " --> pdb=" O ILE a 316 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N THR a 318 " --> pdb=" O ILE a 262 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU a 264 " --> pdb=" O THR a 318 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N LEU a 320 " --> pdb=" O LEU a 264 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL a 203 " --> pdb=" O ILE a 261 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N LEU a 263 " --> pdb=" O VAL a 203 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N MET a 205 " --> pdb=" O LEU a 263 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N ASP a 265 " --> pdb=" O MET a 205 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU a 207 " --> pdb=" O ASP a 265 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL a 228 " --> pdb=" O VAL a 206 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU a 208 " --> pdb=" O VAL a 228 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'b' and resid 79 through 81 removed outlier: 5.950A pdb=" N LYS b 100 " --> pdb=" O VAL b 116 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N VAL b 116 " --> pdb=" O LYS b 100 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'b' and resid 341 through 345 removed outlier: 8.514A pdb=" N GLY b 174 " --> pdb=" O LEU b 313 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE b 315 " --> pdb=" O GLY b 174 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ILE b 176 " --> pdb=" O ILE b 315 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ALA b 317 " --> pdb=" O ILE b 176 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ALA b 178 " --> pdb=" O ALA b 317 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ALA b 319 " --> pdb=" O ALA b 178 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL b 260 " --> pdb=" O THR b 314 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE b 316 " --> pdb=" O VAL b 260 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE b 262 " --> pdb=" O ILE b 316 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N THR b 318 " --> pdb=" O ILE b 262 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU b 264 " --> pdb=" O THR b 318 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N LEU b 320 " --> pdb=" O LEU b 264 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL b 203 " --> pdb=" O ILE b 261 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N LEU b 263 " --> pdb=" O VAL b 203 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N MET b 205 " --> pdb=" O LEU b 263 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N ASP b 265 " --> pdb=" O MET b 205 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU b 207 " --> pdb=" O ASP b 265 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL b 228 " --> pdb=" O VAL b 206 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU b 208 " --> pdb=" O VAL b 228 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'c' and resid 79 through 81 removed outlier: 5.950A pdb=" N LYS c 100 " --> pdb=" O VAL c 116 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N VAL c 116 " --> pdb=" O LYS c 100 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'c' and resid 341 through 345 removed outlier: 8.514A pdb=" N GLY c 174 " --> pdb=" O LEU c 313 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE c 315 " --> pdb=" O GLY c 174 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ILE c 176 " --> pdb=" O ILE c 315 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ALA c 317 " --> pdb=" O ILE c 176 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N ALA c 178 " --> pdb=" O ALA c 317 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ALA c 319 " --> pdb=" O ALA c 178 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL c 260 " --> pdb=" O THR c 314 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ILE c 316 " --> pdb=" O VAL c 260 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE c 262 " --> pdb=" O ILE c 316 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N THR c 318 " --> pdb=" O ILE c 262 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU c 264 " --> pdb=" O THR c 318 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N LEU c 320 " --> pdb=" O LEU c 264 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL c 203 " --> pdb=" O ILE c 261 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N LEU c 263 " --> pdb=" O VAL c 203 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N MET c 205 " --> pdb=" O LEU c 263 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N ASP c 265 " --> pdb=" O MET c 205 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU c 207 " --> pdb=" O ASP c 265 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL c 228 " --> pdb=" O VAL c 206 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU c 208 " --> pdb=" O VAL c 228 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'd' and resid 79 through 81 removed outlier: 5.950A pdb=" N LYS d 100 " --> pdb=" O VAL d 116 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N VAL d 116 " --> pdb=" O LYS d 100 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'd' and resid 341 through 345 removed outlier: 8.514A pdb=" N GLY d 174 " --> pdb=" O LEU d 313 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE d 315 " --> pdb=" O GLY d 174 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ILE d 176 " --> pdb=" O ILE d 315 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ALA d 317 " --> pdb=" O ILE d 176 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ALA d 178 " --> pdb=" O ALA d 317 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ALA d 319 " --> pdb=" O ALA d 178 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL d 260 " --> pdb=" O THR d 314 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE d 316 " --> pdb=" O VAL d 260 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE d 262 " --> pdb=" O ILE d 316 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N THR d 318 " --> pdb=" O ILE d 262 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU d 264 " --> pdb=" O THR d 318 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N LEU d 320 " --> pdb=" O LEU d 264 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL d 203 " --> pdb=" O ILE d 261 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N LEU d 263 " --> pdb=" O VAL d 203 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N MET d 205 " --> pdb=" O LEU d 263 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N ASP d 265 " --> pdb=" O MET d 205 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU d 207 " --> pdb=" O ASP d 265 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL d 228 " --> pdb=" O VAL d 206 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU d 208 " --> pdb=" O VAL d 228 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'e' and resid 79 through 81 removed outlier: 5.950A pdb=" N LYS e 100 " --> pdb=" O VAL e 116 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N VAL e 116 " --> pdb=" O LYS e 100 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'e' and resid 341 through 345 removed outlier: 8.514A pdb=" N GLY e 174 " --> pdb=" O LEU e 313 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE e 315 " --> pdb=" O GLY e 174 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ILE e 176 " --> pdb=" O ILE e 315 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ALA e 317 " --> pdb=" O ILE e 176 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ALA e 178 " --> pdb=" O ALA e 317 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA e 319 " --> pdb=" O ALA e 178 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL e 260 " --> pdb=" O THR e 314 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ILE e 316 " --> pdb=" O VAL e 260 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE e 262 " --> pdb=" O ILE e 316 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N THR e 318 " --> pdb=" O ILE e 262 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU e 264 " --> pdb=" O THR e 318 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N LEU e 320 " --> pdb=" O LEU e 264 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL e 203 " --> pdb=" O ILE e 261 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N LEU e 263 " --> pdb=" O VAL e 203 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N MET e 205 " --> pdb=" O LEU e 263 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ASP e 265 " --> pdb=" O MET e 205 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU e 207 " --> pdb=" O ASP e 265 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL e 228 " --> pdb=" O VAL e 206 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU e 208 " --> pdb=" O VAL e 228 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 149 through 155 removed outlier: 6.160A pdb=" N ALA A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 182 through 186 removed outlier: 7.345A pdb=" N PHE A 196 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 222 through 229 removed outlier: 6.658A pdb=" N ALA A 237 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ALA A 226 " --> pdb=" O LYS A 235 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LYS A 235 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ARG A 228 " --> pdb=" O ARG A 233 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG A 233 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 293 through 299 removed outlier: 6.547A pdb=" N ALA A 308 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE A 296 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASP A 306 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL A 298 " --> pdb=" O THR A 304 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR A 304 " --> pdb=" O VAL A 298 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'U' and resid 12 through 15 removed outlier: 6.396A pdb=" N THR U 27 " --> pdb=" O VAL U 14 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'U' and resid 170 through 172 removed outlier: 7.062A pdb=" N LYS U 145 " --> pdb=" O THR U 57 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL U 59 " --> pdb=" O ARG U 143 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ARG U 143 " --> pdb=" O VAL U 59 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ILE U 61 " --> pdb=" O SER U 141 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N SER U 141 " --> pdb=" O ILE U 61 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'U' and resid 108 through 111 Processing sheet with id= T, first strand: chain 'V' and resid 23 through 28 Processing sheet with id= U, first strand: chain 'V' and resid 90 through 92 Processing sheet with id= V, first strand: chain 'V' and resid 97 through 102 removed outlier: 3.716A pdb=" N MET V 142 " --> pdb=" O LEU V 102 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLN V 147 " --> pdb=" O VAL V 56 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N VAL V 56 " --> pdb=" O GLN V 147 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLY V 149 " --> pdb=" O CYS V 54 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N CYS V 54 " --> pdb=" O GLY V 149 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'X' and resid 93 through 95 Processing sheet with id= X, first strand: chain 'X' and resid 118 through 123 removed outlier: 5.911A pdb=" N ARG X 101 " --> pdb=" O TYR X 70 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N TYR X 70 " --> pdb=" O ARG X 101 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL X 103 " --> pdb=" O LEU X 68 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU X 68 " --> pdb=" O VAL X 103 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'X' and resid 148 through 151 Processing sheet with id= Z, first strand: chain 'X' and resid 154 through 160 Processing sheet with id= AA, first strand: chain 'X' and resid 603 through 606 Processing sheet with id= AB, first strand: chain 'X' and resid 634 through 637 Processing sheet with id= AC, first strand: chain 'X' and resid 748 through 752 removed outlier: 5.695A pdb=" N LYS X 735 " --> pdb=" O VAL X 724 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL X 724 " --> pdb=" O LYS X 735 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'X' and resid 1096 through 1098 Processing sheet with id= AE, first strand: chain 'X' and resid 830 through 841 removed outlier: 3.888A pdb=" N ASP X 930 " --> pdb=" O TYR X1053 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA X1055 " --> pdb=" O VAL X 928 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N VAL X 928 " --> pdb=" O ALA X1055 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'Y' and resid 145 through 147 removed outlier: 3.558A pdb=" N VAL Y 145 " --> pdb=" O LYS Y 179 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP Y 177 " --> pdb=" O ILE Y 147 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'Y' and resid 350 through 354 Processing sheet with id= AH, first strand: chain 'Y' and resid 355 through 358 removed outlier: 6.275A pdb=" N ILE Y 447 " --> pdb=" O THR Y 356 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLY Y 358 " --> pdb=" O ILE Y 447 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU Y 449 " --> pdb=" O GLY Y 358 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'Y' and resid 365 through 369 removed outlier: 5.744A pdb=" N GLU Y 438 " --> pdb=" O CYS Y 366 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU Y 368 " --> pdb=" O GLU Y 438 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL Y 440 " --> pdb=" O LEU Y 368 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'Y' and resid 547 through 557 Processing sheet with id= AK, first strand: chain 'Y' and resid 819 through 823 Processing sheet with id= AL, first strand: chain 'Y' and resid 957 through 961 removed outlier: 3.690A pdb=" N GLU Y 981 " --> pdb=" O SER Y 961 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU Y 993 " --> pdb=" O LEU Y 984 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'Y' and resid 965 through 967 Processing sheet with id= AN, first strand: chain 'Y' and resid 1113 through 1115 removed outlier: 4.048A pdb=" N VAL Y1113 " --> pdb=" O VAL Y1035 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL Y1035 " --> pdb=" O VAL Y1113 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG Y1036 " --> pdb=" O LYS Y1079 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS Y1079 " --> pdb=" O ARG Y1036 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'Y' and resid 1162 through 1164 Processing sheet with id= AP, first strand: chain 'Y' and resid 1173 through 1175 removed outlier: 3.529A pdb=" N LEU Y1175 " --> pdb=" O GLU Y1188 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU Y1188 " --> pdb=" O LEU Y1175 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'Y' and resid 1264 through 1266 1606 hydrogen bonds defined for protein. 4572 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 21.33 Time building geometry restraints manager: 22.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 14463 1.33 - 1.45: 7926 1.45 - 1.57: 29491 1.57 - 1.69: 193 1.69 - 1.81: 408 Bond restraints: 52481 Sorted by residual: bond pdb=" BE BEF a1002 " pdb=" F2 BEF a1002 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.86e+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 1.85e+01 bond pdb=" BE BEF c1002 " pdb=" F2 BEF c1002 " 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 1.562 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" BE BEF b1002 " pdb=" F2 BEF b1002 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.83e+01 ... (remaining 52476 not shown) Histogram of bond angle deviations from ideal: 98.37 - 105.91: 1589 105.91 - 113.45: 29378 113.45 - 120.99: 25296 120.99 - 128.53: 14704 128.53 - 136.07: 259 Bond angle restraints: 71226 Sorted by residual: angle pdb=" C LEU Y 268 " pdb=" N TYR Y 269 " pdb=" CA TYR Y 269 " ideal model delta sigma weight residual 122.06 113.83 8.23 1.86e+00 2.89e-01 1.96e+01 angle pdb=" C SER Y 119 " pdb=" N LEU Y 120 " pdb=" CA LEU Y 120 " ideal model delta sigma weight residual 121.80 132.15 -10.35 2.44e+00 1.68e-01 1.80e+01 angle pdb=" F2 BEF d1002 " pdb=" BE BEF d1002 " pdb=" F3 BEF d1002 " ideal model delta sigma weight residual 119.96 107.27 12.69 3.00e+00 1.11e-01 1.79e+01 angle pdb=" F2 BEF c1002 " pdb=" BE BEF c1002 " pdb=" F3 BEF c1002 " ideal model delta sigma weight residual 119.96 107.30 12.66 3.00e+00 1.11e-01 1.78e+01 angle pdb=" F2 BEF b1002 " pdb=" BE BEF b1002 " pdb=" F3 BEF b1002 " ideal model delta sigma weight residual 119.96 107.36 12.60 3.00e+00 1.11e-01 1.76e+01 ... (remaining 71221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 31219 35.35 - 70.71: 813 70.71 - 106.06: 54 106.06 - 141.41: 5 141.41 - 176.77: 8 Dihedral angle restraints: 32099 sinusoidal: 13941 harmonic: 18158 Sorted by residual: dihedral pdb=" CA LEU Y 120 " pdb=" C LEU Y 120 " pdb=" N PRO Y 121 " pdb=" CA PRO Y 121 " ideal model delta harmonic sigma weight residual 180.00 126.09 53.91 0 5.00e+00 4.00e-02 1.16e+02 dihedral pdb=" C4' U R 23 " pdb=" C3' U R 23 " pdb=" C2' U R 23 " pdb=" C1' U R 23 " ideal model delta sinusoidal sigma weight residual -35.00 34.87 -69.87 1 8.00e+00 1.56e-02 9.84e+01 dihedral pdb=" C5' U R 23 " pdb=" C4' U R 23 " pdb=" C3' U R 23 " pdb=" O3' U R 23 " ideal model delta sinusoidal sigma weight residual 147.00 81.08 65.92 1 8.00e+00 1.56e-02 8.88e+01 ... (remaining 32096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 7022 0.058 - 0.116: 1064 0.116 - 0.175: 63 0.175 - 0.233: 2 0.233 - 0.291: 1 Chirality restraints: 8152 Sorted by residual: chirality pdb=" C3' U R 23 " pdb=" C4' U R 23 " pdb=" O3' U R 23 " pdb=" C2' U R 23 " both_signs ideal model delta sigma weight residual False -2.74 -2.45 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C2' U R 23 " pdb=" C3' U R 23 " pdb=" O2' U R 23 " pdb=" C1' U R 23 " both_signs ideal model delta sigma weight residual False -2.52 -2.75 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA TYR Y 269 " pdb=" N TYR Y 269 " pdb=" C TYR Y 269 " pdb=" CB TYR Y 269 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 8149 not shown) Planarity restraints: 8987 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU Y 120 " 0.061 5.00e-02 4.00e+02 9.29e-02 1.38e+01 pdb=" N PRO Y 121 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO Y 121 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO Y 121 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU Y 658 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.64e+00 pdb=" C GLU Y 658 " -0.033 2.00e-02 2.50e+03 pdb=" O GLU Y 658 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA Y 659 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO Y 288 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.63e+00 pdb=" C PRO Y 288 " -0.033 2.00e-02 2.50e+03 pdb=" O PRO Y 288 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP Y 289 " 0.011 2.00e-02 2.50e+03 ... (remaining 8984 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 599 2.54 - 3.13: 41283 3.13 - 3.72: 84503 3.72 - 4.31: 113265 4.31 - 4.90: 179628 Nonbonded interactions: 419278 Sorted by model distance: nonbonded pdb=" O1B ADP a1000 " pdb="MG MG a1001 " model vdw 1.954 2.170 nonbonded pdb="MG MG a1001 " pdb=" O HOH a1101 " model vdw 1.981 2.170 nonbonded pdb=" O2B ADP d1000 " pdb="MG MG d1001 " model vdw 1.991 2.170 nonbonded pdb=" OG1 THR a 185 " pdb="MG MG a1001 " model vdw 2.003 2.170 nonbonded pdb=" O2B ADP e1000 " pdb="MG MG e1001 " model vdw 2.009 2.170 ... (remaining 419273 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' and resid 1 through 417) 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' } 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 102 5.49 5 Mg 6 5.21 5 S 223 5.16 5 Be 5 3.05 5 C 31985 2.51 5 N 9103 2.21 5 O 10112 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: 1.900 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: 10.700 Check model and map are aligned: 0.690 Convert atoms to be neutral: 0.410 Process input model: 142.080 Find NCS groups from input model: 2.550 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 161.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 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 0.086 52481 Z= 0.167 Angle : 0.588 12.688 71226 Z= 0.323 Chirality : 0.041 0.291 8152 Planarity : 0.004 0.093 8987 Dihedral : 15.200 176.765 20377 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.64 % Favored : 95.34 % Rotamer Outliers : 3.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.12 % Twisted Proline : 0.40 % 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: -3.15 (0.09), residues: 6289 helix: -1.23 (0.10), residues: 2316 sheet: -2.14 (0.15), residues: 800 loop : -2.79 (0.10), residues: 3173 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 385 time to evaluate : 5.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 168 outliers final: 33 residues processed: 535 average time/residue: 0.6725 time to fit residues: 586.6651 Evaluate side-chains 304 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 271 time to evaluate : 5.863 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.4478 time to fit residues: 35.9496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 534 optimal weight: 20.0000 chunk 479 optimal weight: 7.9990 chunk 266 optimal weight: 7.9990 chunk 163 optimal weight: 3.9990 chunk 323 optimal weight: 10.0000 chunk 256 optimal weight: 10.0000 chunk 496 optimal weight: 9.9990 chunk 191 optimal weight: 8.9990 chunk 301 optimal weight: 0.9990 chunk 369 optimal weight: 9.9990 chunk 574 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 42 HIS f 256 HIS f 401 ASN a 199 HIS ** a 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 401 ASN b 256 HIS b 401 ASN c 190 ASN ** c 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 275 ASN c 401 ASN d 220 GLN d 241 GLN d 256 HIS d 401 ASN e 220 GLN ** e 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 275 ASN e 401 ASN A 70 GLN A 88 ASN A 157 ASN ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 ASN A 324 ASN A 330 GLN A 349 GLN A 412 ASN A 428 ASN A 462 GLN U 37 HIS U 132 HIS U 147 GLN V 93 GLN V 103 ASN V 194 GLN W 43 ASN X 41 GLN ** X 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 214 ASN X 238 GLN X 343 HIS X 463 GLN X 604 HIS ** X 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 808 ASN X 932 GLN X1008 GLN ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1013 GLN ** X1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1061 GLN X1256 GLN X1314 GLN Y 80 HIS ** Y 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 335 GLN Y 365 GLN Y 488 ASN Y 545 HIS Y 702 GLN ** Y 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 865 HIS Y1295 ASN Y1326 GLN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 52481 Z= 0.295 Angle : 0.657 13.168 71226 Z= 0.333 Chirality : 0.041 0.253 8152 Planarity : 0.004 0.095 8987 Dihedral : 12.292 175.961 7898 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 22.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.12 % Twisted Proline : 0.40 % 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: -2.10 (0.10), residues: 6289 helix: -0.16 (0.11), residues: 2281 sheet: -1.92 (0.15), residues: 843 loop : -2.20 (0.10), residues: 3165 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 287 time to evaluate : 6.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 5 outliers final: 1 residues processed: 292 average time/residue: 0.6644 time to fit residues: 322.6313 Evaluate side-chains 246 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 245 time to evaluate : 6.004 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5241 time to fit residues: 9.0798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 319 optimal weight: 1.9990 chunk 178 optimal weight: 30.0000 chunk 478 optimal weight: 2.9990 chunk 391 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 575 optimal weight: 20.0000 chunk 622 optimal weight: 2.9990 chunk 512 optimal weight: 9.9990 chunk 571 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 461 optimal weight: 0.0050 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 190 ASN f 241 GLN a 42 HIS a 256 HIS b 42 HIS b 135 ASN c 42 HIS c 256 HIS ** c 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 401 ASN d 42 HIS ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 135 ASN ** e 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 ASN ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 GLN A 324 ASN V 103 ASN ** X 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 488 ASN Y 805 GLN ** Y 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1244 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 52481 Z= 0.165 Angle : 0.539 9.339 71226 Z= 0.270 Chirality : 0.040 0.218 8152 Planarity : 0.004 0.095 8987 Dihedral : 12.109 176.598 7898 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.12 % Twisted Proline : 0.40 % 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: -1.56 (0.10), residues: 6289 helix: 0.38 (0.11), residues: 2306 sheet: -1.64 (0.16), residues: 846 loop : -1.98 (0.11), residues: 3137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 285 time to evaluate : 5.911 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: 2 outliers final: 0 residues processed: 287 average time/residue: 0.6688 time to fit residues: 321.8676 Evaluate side-chains 245 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 5.652 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.5006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 568 optimal weight: 10.0000 chunk 432 optimal weight: 7.9990 chunk 298 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 274 optimal weight: 40.0000 chunk 386 optimal weight: 6.9990 chunk 577 optimal weight: 0.2980 chunk 611 optimal weight: 4.9990 chunk 301 optimal weight: 9.9990 chunk 547 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 190 ASN b 190 ASN ** c 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 190 ASN ** e 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 103 ASN ** X 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 832 HIS ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1023 HIS ** Y 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 805 GLN ** Y 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 52481 Z= 0.212 Angle : 0.572 9.261 71226 Z= 0.286 Chirality : 0.040 0.205 8152 Planarity : 0.004 0.097 8987 Dihedral : 12.105 174.520 7898 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.12 % Twisted Proline : 0.40 % 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: -1.24 (0.11), residues: 6289 helix: 0.66 (0.11), residues: 2281 sheet: -1.49 (0.16), residues: 874 loop : -1.78 (0.11), residues: 3134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 270 time to evaluate : 5.681 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: 4 outliers final: 1 residues processed: 274 average time/residue: 0.6753 time to fit residues: 311.7125 Evaluate side-chains 243 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 242 time to evaluate : 6.673 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.7832 time to fit residues: 10.3941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 509 optimal weight: 5.9990 chunk 347 optimal weight: 20.0000 chunk 8 optimal weight: 3.9990 chunk 455 optimal weight: 0.0060 chunk 252 optimal weight: 2.9990 chunk 522 optimal weight: 8.9990 chunk 422 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 312 optimal weight: 8.9990 chunk 549 optimal weight: 8.9990 chunk 154 optimal weight: 8.9990 overall best weight: 4.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 275 ASN ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 ASN W 73 GLN ** X 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X1157 GLN ** Y 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 335 GLN ** Y 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 805 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 52481 Z= 0.212 Angle : 0.573 10.410 71226 Z= 0.288 Chirality : 0.040 0.230 8152 Planarity : 0.004 0.095 8987 Dihedral : 12.112 173.056 7898 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 20.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.12 % Twisted Proline : 0.40 % 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: -1.06 (0.11), residues: 6289 helix: 0.71 (0.11), residues: 2288 sheet: -1.36 (0.17), residues: 855 loop : -1.60 (0.11), residues: 3146 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 264 time to evaluate : 6.317 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 outliers start: 2 outliers final: 2 residues processed: 266 average time/residue: 0.6709 time to fit residues: 305.3625 Evaluate side-chains 242 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 240 time to evaluate : 5.875 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5439 time to fit residues: 10.8327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 205 optimal weight: 20.0000 chunk 551 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 359 optimal weight: 0.0370 chunk 151 optimal weight: 20.0000 chunk 612 optimal weight: 6.9990 chunk 508 optimal weight: 20.0000 chunk 283 optimal weight: 40.0000 chunk 50 optimal weight: 20.0000 chunk 202 optimal weight: 2.9990 chunk 321 optimal weight: 10.0000 overall best weight: 5.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 344 HIS a 90 ASN c 241 GLN ** c 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 256 HIS d 275 ASN ** e 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 190 ASN A 70 GLN ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 238 GLN ** X 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 805 GLN ** Y 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 52481 Z= 0.251 Angle : 0.605 9.179 71226 Z= 0.306 Chirality : 0.041 0.225 8152 Planarity : 0.004 0.097 8987 Dihedral : 12.137 178.460 7898 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 23.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.12 % Twisted Proline : 0.40 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.11), residues: 6289 helix: 0.73 (0.11), residues: 2298 sheet: -1.35 (0.17), residues: 872 loop : -1.53 (0.11), residues: 3119 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 6.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 258 average time/residue: 0.6455 time to fit residues: 285.7844 Evaluate side-chains 235 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 6.254 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.4149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 590 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 348 optimal weight: 9.9990 chunk 447 optimal weight: 8.9990 chunk 346 optimal weight: 0.9980 chunk 515 optimal weight: 5.9990 chunk 341 optimal weight: 10.0000 chunk 610 optimal weight: 0.6980 chunk 381 optimal weight: 20.0000 chunk 371 optimal weight: 20.0000 chunk 281 optimal weight: 6.9990 overall best weight: 4.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 275 ASN ** b 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 190 ASN A 70 GLN ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 37 HIS V 208 ASN ** X 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 238 GLN ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 628 HIS ** X 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 761 GLN ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 805 GLN ** Y 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1227 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 52481 Z= 0.239 Angle : 0.598 9.789 71226 Z= 0.301 Chirality : 0.041 0.226 8152 Planarity : 0.004 0.096 8987 Dihedral : 12.111 173.733 7898 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 22.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.12 % Twisted Proline : 0.40 % 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: -0.94 (0.11), residues: 6289 helix: 0.71 (0.11), residues: 2312 sheet: -1.29 (0.17), residues: 859 loop : -1.46 (0.11), residues: 3118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 5.373 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 outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.6380 time to fit residues: 277.8880 Evaluate side-chains 234 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 6.107 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.1388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 377 optimal weight: 0.9990 chunk 243 optimal weight: 9.9990 chunk 364 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 387 optimal weight: 7.9990 chunk 415 optimal weight: 2.9990 chunk 301 optimal weight: 0.0020 chunk 56 optimal weight: 20.0000 chunk 479 optimal weight: 4.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 190 ASN ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 760 ASN ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 450 HIS ** Y 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 52481 Z= 0.159 Angle : 0.561 10.405 71226 Z= 0.279 Chirality : 0.041 0.227 8152 Planarity : 0.004 0.092 8987 Dihedral : 11.872 173.737 7898 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.63 % Favored : 95.36 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.12 % Twisted Proline : 0.40 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.11), residues: 6289 helix: 0.88 (0.11), residues: 2305 sheet: -1.18 (0.17), residues: 847 loop : -1.36 (0.11), residues: 3137 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 5.858 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 outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.6469 time to fit residues: 281.6054 Evaluate side-chains 237 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 5.962 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.0591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 554 optimal weight: 0.9990 chunk 584 optimal weight: 30.0000 chunk 533 optimal weight: 5.9990 chunk 568 optimal weight: 10.0000 chunk 342 optimal weight: 0.0670 chunk 247 optimal weight: 4.9990 chunk 446 optimal weight: 7.9990 chunk 174 optimal weight: 7.9990 chunk 513 optimal weight: 0.9980 chunk 537 optimal weight: 0.4980 chunk 566 optimal weight: 8.9990 overall best weight: 1.5122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 193 GLN ** b 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 965 GLN ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 52481 Z= 0.146 Angle : 0.558 10.689 71226 Z= 0.276 Chirality : 0.041 0.238 8152 Planarity : 0.004 0.092 8987 Dihedral : 11.670 173.735 7898 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.12 % Twisted Proline : 0.40 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.11), residues: 6289 helix: 0.95 (0.11), residues: 2300 sheet: -1.07 (0.17), residues: 870 loop : -1.30 (0.11), residues: 3119 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 6.270 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 outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.6579 time to fit residues: 289.8953 Evaluate side-chains 234 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 6.148 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.2455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 373 optimal weight: 4.9990 chunk 601 optimal weight: 5.9990 chunk 366 optimal weight: 5.9990 chunk 285 optimal weight: 0.4980 chunk 417 optimal weight: 4.9990 chunk 630 optimal weight: 30.0000 chunk 580 optimal weight: 0.9980 chunk 502 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 chunk 387 optimal weight: 7.9990 chunk 307 optimal weight: 6.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 90 ASN a 241 GLN ** a 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 275 ASN A 70 GLN ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 965 GLN ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 805 GLN ** Y 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 52481 Z= 0.194 Angle : 0.580 13.429 71226 Z= 0.289 Chirality : 0.041 0.240 8152 Planarity : 0.004 0.092 8987 Dihedral : 11.703 173.573 7898 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 20.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.93 % Favored : 95.05 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.12 % Twisted Proline : 0.40 % 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: -0.61 (0.11), residues: 6289 helix: 0.98 (0.11), residues: 2309 sheet: -1.06 (0.17), residues: 888 loop : -1.27 (0.11), residues: 3092 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 5.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.6432 time to fit residues: 275.1010 Evaluate side-chains 233 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 5.969 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.8196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 398 optimal weight: 6.9990 chunk 534 optimal weight: 9.9990 chunk 153 optimal weight: 8.9990 chunk 463 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 502 optimal weight: 6.9990 chunk 210 optimal weight: 3.9990 chunk 516 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 327 GLN ** X 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 965 GLN ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1257 GLN ** Y 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 805 GLN ** Y 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.034973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.022548 restraints weight = 698122.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.022827 restraints weight = 472332.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.023188 restraints weight = 358941.898| |-----------------------------------------------------------------------------| r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.5652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 52481 Z= 0.227 Angle : 0.612 10.569 71226 Z= 0.306 Chirality : 0.041 0.228 8152 Planarity : 0.004 0.095 8987 Dihedral : 11.768 173.028 7898 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 23.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.12 % Twisted Proline : 0.40 % 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: -0.74 (0.11), residues: 6289 helix: 0.79 (0.11), residues: 2357 sheet: -1.09 (0.17), residues: 885 loop : -1.32 (0.11), residues: 3047 =============================================================================== Job complete usr+sys time: 8257.95 seconds wall clock time: 152 minutes 20.23 seconds (9140.23 seconds total)