Starting phenix.real_space_refine on Sun Feb 25 12:49:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ade_11725/02_2024/7ade_11725_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ade_11725/02_2024/7ade_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_11725/02_2024/7ade_11725.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ade_11725/02_2024/7ade_11725.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ade_11725/02_2024/7ade_11725_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ade_11725/02_2024/7ade_11725_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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 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. 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: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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 dihedrals: 1 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: 25.63, per 1000 atoms: 0.50 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: 20.09 Conformation dependent library (CDL) restraints added in 8.6 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: 23.08 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: 21.19 Time building geometry restraints manager: 21.65 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: 31315 35.35 - 70.71: 865 70.71 - 106.06: 65 106.06 - 141.41: 5 141.41 - 176.77: 8 Dihedral angle restraints: 32258 sinusoidal: 14100 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 32255 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 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 8.160 Check model and map are aligned: 0.740 Set scattering table: 0.440 Process input model: 149.570 Find NCS groups from input model: 2.490 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 166.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 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 : 15.512 176.765 20536 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.64 % Favored : 95.34 % Rotamer: Outliers : 3.12 % Allowed : 5.80 % Favored : 91.08 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP X1276 HIS 0.003 0.000 HIS b 239 PHE 0.021 0.001 PHE Y 141 TYR 0.020 0.001 TYR Y 269 ARG 0.002 0.000 ARG A 51 *********************** 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 : 5.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 186 MET cc_start: 0.8763 (pmm) cc_final: 0.8379 (pmm) REVERT: f 217 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.8706 (p) REVERT: f 396 MET cc_start: 0.8848 (tpt) cc_final: 0.8558 (tpp) REVERT: b 31 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8731 (tmtt) REVERT: c 21 MET cc_start: 0.8439 (mmm) cc_final: 0.8044 (mtt) REVERT: c 137 THR cc_start: 0.7897 (OUTLIER) cc_final: 0.5231 (t) REVERT: d 266 SER cc_start: 0.6825 (OUTLIER) cc_final: 0.6542 (t) REVERT: d 318 THR cc_start: 0.8132 (OUTLIER) cc_final: 0.7925 (p) REVERT: e 186 MET cc_start: 0.8501 (pmm) cc_final: 0.8251 (pmm) REVERT: e 266 SER cc_start: 0.6420 (OUTLIER) cc_final: 0.4573 (t) REVERT: e 312 SER cc_start: 0.6341 (OUTLIER) cc_final: 0.5528 (t) REVERT: e 320 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9104 (mm) REVERT: e 374 GLN cc_start: 0.9365 (OUTLIER) cc_final: 0.9089 (mm110) REVERT: e 396 MET cc_start: 0.9287 (tpt) cc_final: 0.9059 (mmm) REVERT: A 288 MET cc_start: 0.7497 (mtm) cc_final: 0.6497 (ppp) REVERT: A 334 TRP cc_start: 0.7827 (m-10) cc_final: 0.7080 (m-10) REVERT: A 339 MET cc_start: 0.6063 (mmt) cc_final: 0.5244 (mpp) REVERT: V 236 ASP cc_start: 0.8138 (m-30) cc_final: 0.7794 (p0) REVERT: W 22 VAL cc_start: 0.9580 (t) cc_final: 0.9311 (t) REVERT: W 26 ARG cc_start: 0.9378 (tpt90) cc_final: 0.9160 (tpt90) REVERT: W 30 MET cc_start: 0.9378 (ptm) cc_final: 0.9058 (ptm) REVERT: W 39 VAL cc_start: 0.7339 (t) cc_final: 0.6707 (p) REVERT: W 53 GLU cc_start: 0.8904 (pt0) cc_final: 0.8492 (mt-10) REVERT: W 61 ASN cc_start: 0.9061 (t0) cc_final: 0.8836 (t0) REVERT: W 64 LEU cc_start: 0.8116 (pp) cc_final: 0.7834 (pp) REVERT: X 1230 MET cc_start: 0.6392 (ttm) cc_final: 0.5803 (ttm) REVERT: Y 115 TRP cc_start: 0.8970 (m-10) cc_final: 0.8686 (m-10) REVERT: Y 166 LEU cc_start: 0.9067 (tp) cc_final: 0.8762 (pp) outliers start: 168 outliers final: 33 residues processed: 535 average time/residue: 0.6644 time to fit residues: 581.3811 Evaluate side-chains 316 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 274 time to evaluate : 6.343 ------------------------------------------------------------------------------- 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: 10.0000 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: 0.0070 chunk 301 optimal weight: 0.9990 chunk 369 optimal weight: 9.9990 chunk 574 optimal weight: 8.9990 overall best weight: 4.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 256 HIS f 401 ASN a 256 HIS a 401 ASN b 256 HIS b 401 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 A 313 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 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 343 HIS X 463 GLN X 604 HIS ** X 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 808 ASN X 932 GLN X1008 GLN ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1013 GLN 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 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 488 ASN Y 545 HIS Y 702 GLN Y 805 GLN Y 865 HIS Y1326 GLN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 52481 Z= 0.237 Angle : 0.593 10.676 71226 Z= 0.299 Chirality : 0.040 0.218 8152 Planarity : 0.004 0.092 8987 Dihedral : 13.053 177.302 8057 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.15 % Allowed : 4.46 % Favored : 95.39 % 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: -2.05 (0.10), residues: 6289 helix: -0.03 (0.11), residues: 2304 sheet: -1.87 (0.16), residues: 823 loop : -2.28 (0.10), residues: 3162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP Y1020 HIS 0.006 0.001 HIS c 42 PHE 0.026 0.001 PHE A 359 TYR 0.026 0.001 TYR Y 269 ARG 0.022 0.001 ARG Y 481 *********************** 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 304 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 296 time to evaluate : 5.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 219 MET cc_start: 0.8164 (mmp) cc_final: 0.7924 (mmm) REVERT: f 396 MET cc_start: 0.8931 (tpt) cc_final: 0.8637 (tpp) REVERT: a 343 LEU cc_start: 0.8742 (mt) cc_final: 0.8506 (mt) REVERT: b 21 MET cc_start: 0.6952 (mtp) cc_final: 0.6464 (mtp) REVERT: b 29 MET cc_start: 0.8535 (ptm) cc_final: 0.7935 (ptt) REVERT: b 380 MET cc_start: 0.9036 (mtm) cc_final: 0.8715 (mtm) REVERT: b 396 MET cc_start: 0.8764 (mmp) cc_final: 0.8535 (mmm) REVERT: c 21 MET cc_start: 0.8597 (mmm) cc_final: 0.8306 (mtt) REVERT: c 219 MET cc_start: 0.7842 (tpp) cc_final: 0.7623 (mmm) REVERT: d 29 MET cc_start: 0.7945 (pmm) cc_final: 0.7717 (pmm) REVERT: d 186 MET cc_start: 0.8725 (ptp) cc_final: 0.8521 (ptp) REVERT: e 186 MET cc_start: 0.8557 (pmm) cc_final: 0.8292 (pmm) REVERT: e 396 MET cc_start: 0.9408 (tpt) cc_final: 0.9065 (mmm) REVERT: e 405 MET cc_start: 0.9468 (ptt) cc_final: 0.9260 (pmm) REVERT: A 288 MET cc_start: 0.7266 (mtm) cc_final: 0.6466 (ppp) REVERT: A 334 TRP cc_start: 0.7752 (m-10) cc_final: 0.7445 (m-10) REVERT: A 339 MET cc_start: 0.6089 (mmt) cc_final: 0.5327 (mpp) REVERT: A 428 ASN cc_start: -0.1184 (OUTLIER) cc_final: -0.1927 (p0) REVERT: V 103 ASN cc_start: 0.8149 (m110) cc_final: 0.7916 (m-40) REVERT: V 236 ASP cc_start: 0.8278 (m-30) cc_final: 0.7817 (p0) REVERT: W 26 ARG cc_start: 0.9571 (tpt90) cc_final: 0.9022 (tpt90) REVERT: W 30 MET cc_start: 0.9233 (ptm) cc_final: 0.8963 (ptm) REVERT: W 64 LEU cc_start: 0.7912 (pp) cc_final: 0.7656 (pp) REVERT: X 681 MET cc_start: 0.8462 (pmm) cc_final: 0.8141 (pmm) REVERT: Y 166 LEU cc_start: 0.9216 (tp) cc_final: 0.8924 (pp) REVERT: Y 192 MET cc_start: 0.8380 (mmp) cc_final: 0.7781 (mmm) REVERT: Y 697 MET cc_start: 0.8320 (ttp) cc_final: 0.7928 (ttm) REVERT: Y 1040 MET cc_start: 0.6573 (mtm) cc_final: 0.5781 (mpp) REVERT: Y 1141 VAL cc_start: 0.9499 (OUTLIER) cc_final: 0.8864 (m) REVERT: Y 1145 PHE cc_start: 0.7728 (m-80) cc_final: 0.7152 (m-80) REVERT: Y 1260 MET cc_start: 0.7717 (tpt) cc_final: 0.7362 (tpt) outliers start: 8 outliers final: 3 residues processed: 304 average time/residue: 0.6821 time to fit residues: 345.8221 Evaluate side-chains 258 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 253 time to evaluate : 5.872 ------------------------------------------------------------------------------- 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: 20.0000 chunk 178 optimal weight: 40.0000 chunk 478 optimal weight: 4.9990 chunk 391 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 575 optimal weight: 10.0000 chunk 622 optimal weight: 8.9990 chunk 512 optimal weight: 6.9990 chunk 571 optimal weight: 9.9990 chunk 196 optimal weight: 5.9990 chunk 461 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 42 HIS f 190 ASN a 42 HIS a 190 ASN ** a 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 HIS b 190 ASN c 42 HIS ** c 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 190 ASN ** c 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 401 ASN ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 190 ASN ** d 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 401 ASN ** e 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 70 GLN A 88 ASN A 324 ASN A 428 ASN ** V 147 GLN ** 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 832 HIS ** X1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1023 HIS X1209 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 488 ASN Y 702 GLN ** Y 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1244 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 52481 Z= 0.289 Angle : 0.641 15.359 71226 Z= 0.326 Chirality : 0.041 0.211 8152 Planarity : 0.004 0.097 8987 Dihedral : 13.260 179.660 8057 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 23.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.02 % Allowed : 5.11 % Favored : 94.87 % 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: -1.65 (0.10), residues: 6289 helix: 0.25 (0.11), residues: 2309 sheet: -1.70 (0.16), residues: 872 loop : -1.98 (0.11), residues: 3108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y 115 HIS 0.007 0.001 HIS Y 777 PHE 0.038 0.002 PHE f 412 TYR 0.022 0.002 TYR Y 269 ARG 0.013 0.001 ARG V 170 *********************** 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 272 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 271 time to evaluate : 6.560 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: f 390 MET cc_start: 0.8168 (ptm) cc_final: 0.7755 (tmm) REVERT: f 396 MET cc_start: 0.8799 (tpt) cc_final: 0.8466 (tpp) REVERT: f 405 MET cc_start: 0.8476 (ptt) cc_final: 0.8233 (ppp) REVERT: a 245 MET cc_start: 0.8461 (mmm) cc_final: 0.8216 (mmm) REVERT: a 343 LEU cc_start: 0.8858 (mt) cc_final: 0.8537 (mt) REVERT: b 1 MET cc_start: 0.8497 (ppp) cc_final: 0.7766 (ppp) REVERT: b 29 MET cc_start: 0.8472 (ptm) cc_final: 0.7890 (ptt) REVERT: b 380 MET cc_start: 0.9030 (mtm) cc_final: 0.8652 (mtp) REVERT: b 390 MET cc_start: 0.8411 (ptm) cc_final: 0.7671 (ptt) REVERT: c 1 MET cc_start: 0.7940 (ppp) cc_final: 0.7591 (ppp) REVERT: c 21 MET cc_start: 0.8955 (mmm) cc_final: 0.8752 (mtt) REVERT: c 29 MET cc_start: 0.8957 (ptm) cc_final: 0.8321 (ptt) REVERT: c 380 MET cc_start: 0.9017 (mtm) cc_final: 0.8671 (mtp) REVERT: e 21 MET cc_start: 0.9042 (mtp) cc_final: 0.8751 (tpp) REVERT: e 186 MET cc_start: 0.8685 (pmm) cc_final: 0.8356 (pmm) REVERT: e 396 MET cc_start: 0.9465 (tpt) cc_final: 0.9058 (mmp) REVERT: e 416 MET cc_start: 0.7834 (ptt) cc_final: 0.6796 (ptt) REVERT: A 288 MET cc_start: 0.7627 (mtm) cc_final: 0.7076 (ppp) REVERT: A 339 MET cc_start: 0.6391 (mmt) cc_final: 0.5497 (mpp) REVERT: V 236 ASP cc_start: 0.8183 (m-30) cc_final: 0.7781 (p0) REVERT: X 315 MET cc_start: 0.9070 (tpp) cc_final: 0.8763 (mmm) REVERT: X 681 MET cc_start: 0.8644 (pmm) cc_final: 0.8167 (pmm) REVERT: Y 166 LEU cc_start: 0.9389 (tp) cc_final: 0.9163 (pp) REVERT: Y 192 MET cc_start: 0.8426 (mmp) cc_final: 0.7783 (mmm) REVERT: Y 484 MET cc_start: 0.8076 (mmp) cc_final: 0.7632 (mmm) REVERT: Y 1040 MET cc_start: 0.7058 (mtm) cc_final: 0.6096 (mtm) REVERT: Y 1145 PHE cc_start: 0.8264 (m-80) cc_final: 0.7590 (m-80) REVERT: Y 1260 MET cc_start: 0.7934 (tpt) cc_final: 0.7459 (tpp) outliers start: 1 outliers final: 0 residues processed: 272 average time/residue: 0.6616 time to fit residues: 303.7168 Evaluate side-chains 239 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 5.871 ------------------------------------------------------------------------------- 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: 9.9990 chunk 432 optimal weight: 7.9990 chunk 298 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 274 optimal weight: 30.0000 chunk 386 optimal weight: 6.9990 chunk 577 optimal weight: 6.9990 chunk 611 optimal weight: 5.9990 chunk 301 optimal weight: 7.9990 chunk 547 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 199 HIS f 344 HIS a 90 ASN a 241 GLN a 275 ASN ** b 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 275 ASN ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 241 GLN ** c 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 344 HIS ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 256 HIS d 275 ASN e 135 ASN ** e 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 295 HIS ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 702 GLN Y 805 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 52481 Z= 0.333 Angle : 0.689 13.344 71226 Z= 0.352 Chirality : 0.042 0.221 8152 Planarity : 0.005 0.102 8987 Dihedral : 13.331 172.694 8057 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 27.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.06 % Allowed : 4.31 % Favored : 95.63 % 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: -1.62 (0.10), residues: 6289 helix: 0.11 (0.11), residues: 2349 sheet: -1.64 (0.16), residues: 873 loop : -1.86 (0.11), residues: 3067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP X 997 HIS 0.008 0.001 HIS Y 777 PHE 0.027 0.002 PHE f 412 TYR 0.025 0.002 TYR Y 631 ARG 0.009 0.001 ARG Y 275 *********************** 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 257 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 254 time to evaluate : 6.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 21 MET cc_start: -0.5048 (mmt) cc_final: -0.5369 (mmt) REVERT: f 219 MET cc_start: 0.8484 (mmp) cc_final: 0.7988 (mmm) REVERT: f 390 MET cc_start: 0.7970 (ptm) cc_final: 0.7738 (ptm) REVERT: f 396 MET cc_start: 0.8906 (tpt) cc_final: 0.8540 (mmm) REVERT: f 405 MET cc_start: 0.8738 (ptt) cc_final: 0.8282 (ppp) REVERT: a 245 MET cc_start: 0.8531 (mmm) cc_final: 0.8105 (mmm) REVERT: a 327 MET cc_start: 0.8787 (mpp) cc_final: 0.8555 (mpp) REVERT: a 341 MET cc_start: 0.8064 (tmm) cc_final: 0.7493 (tmm) REVERT: a 343 LEU cc_start: 0.8804 (mt) cc_final: 0.8579 (mt) REVERT: b 1 MET cc_start: 0.8595 (ppp) cc_final: 0.8182 (ppp) REVERT: b 29 MET cc_start: 0.8577 (ptm) cc_final: 0.7896 (ptt) REVERT: b 380 MET cc_start: 0.9065 (mtm) cc_final: 0.8666 (mtp) REVERT: c 21 MET cc_start: 0.9083 (mmm) cc_final: 0.8879 (mtt) REVERT: c 29 MET cc_start: 0.8808 (ptm) cc_final: 0.8515 (ptt) REVERT: c 327 MET cc_start: 0.8092 (mmm) cc_final: 0.7737 (mmm) REVERT: c 380 MET cc_start: 0.8978 (mtm) cc_final: 0.8614 (mtp) REVERT: d 29 MET cc_start: 0.7598 (pmm) cc_final: 0.7385 (pmm) REVERT: d 205 MET cc_start: 0.8766 (mmm) cc_final: 0.8556 (mmp) REVERT: e 147 MET cc_start: 0.8657 (mmp) cc_final: 0.8377 (mmm) REVERT: e 197 TYR cc_start: 0.9090 (t80) cc_final: 0.8881 (t80) REVERT: e 416 MET cc_start: 0.8310 (ptt) cc_final: 0.7392 (ptt) REVERT: A 339 MET cc_start: 0.6595 (mmt) cc_final: 0.5546 (mpp) REVERT: V 236 ASP cc_start: 0.8293 (m-30) cc_final: 0.7749 (p0) REVERT: W 26 ARG cc_start: 0.9688 (tpt90) cc_final: 0.8925 (tpt90) REVERT: W 30 MET cc_start: 0.9235 (ptp) cc_final: 0.8859 (ptt) REVERT: X 315 MET cc_start: 0.9050 (tpp) cc_final: 0.8676 (mmm) REVERT: Y 166 LEU cc_start: 0.9478 (tp) cc_final: 0.9246 (pp) REVERT: Y 1145 PHE cc_start: 0.8508 (m-80) cc_final: 0.7724 (m-80) REVERT: Y 1260 MET cc_start: 0.8033 (tpt) cc_final: 0.7604 (tpp) outliers start: 3 outliers final: 1 residues processed: 257 average time/residue: 0.6598 time to fit residues: 286.7883 Evaluate side-chains 235 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 234 time to evaluate : 5.710 ------------------------------------------------------------------------------- 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: 9.9990 chunk 347 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 455 optimal weight: 10.0000 chunk 252 optimal weight: 10.0000 chunk 522 optimal weight: 4.9990 chunk 422 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 312 optimal weight: 4.9990 chunk 549 optimal weight: 0.3980 chunk 154 optimal weight: 9.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 275 ASN ** a 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 190 ASN A 70 GLN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 72 GLN ** 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 628 HIS ** 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** ** 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** Y1227 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 52481 Z= 0.215 Angle : 0.587 10.793 71226 Z= 0.297 Chirality : 0.041 0.229 8152 Planarity : 0.004 0.098 8987 Dihedral : 13.154 173.172 8057 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 22.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % 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: 0.49 (0.11), residues: 2313 sheet: -1.54 (0.16), residues: 869 loop : -1.63 (0.11), residues: 3107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 115 HIS 0.006 0.001 HIS Y 777 PHE 0.024 0.001 PHE f 412 TYR 0.030 0.001 TYR Y 269 ARG 0.009 0.000 ARG f 221 *********************** 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 253 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 5.780 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: f 219 MET cc_start: 0.8488 (mmp) cc_final: 0.8065 (mmm) REVERT: f 396 MET cc_start: 0.8944 (tpt) cc_final: 0.8691 (tpp) REVERT: f 416 MET cc_start: 0.9265 (mpp) cc_final: 0.9038 (mpp) REVERT: a 245 MET cc_start: 0.8565 (mmm) cc_final: 0.8088 (mmm) REVERT: a 341 MET cc_start: 0.8022 (tmm) cc_final: 0.7438 (tmm) REVERT: a 343 LEU cc_start: 0.8840 (mt) cc_final: 0.8591 (mt) REVERT: b 1 MET cc_start: 0.8525 (ppp) cc_final: 0.8226 (ppp) REVERT: b 29 MET cc_start: 0.8348 (ptm) cc_final: 0.7841 (ptt) REVERT: b 219 MET cc_start: 0.8167 (mmp) cc_final: 0.7955 (mmm) REVERT: b 380 MET cc_start: 0.9097 (mtm) cc_final: 0.8585 (ptp) REVERT: c 29 MET cc_start: 0.8809 (ptm) cc_final: 0.8030 (ptt) REVERT: c 327 MET cc_start: 0.8126 (mmm) cc_final: 0.7719 (mmm) REVERT: c 380 MET cc_start: 0.8996 (mtm) cc_final: 0.8664 (mtp) REVERT: d 205 MET cc_start: 0.8684 (mmm) cc_final: 0.8302 (mmm) REVERT: d 219 MET cc_start: 0.7634 (mmp) cc_final: 0.6876 (mmm) REVERT: e 396 MET cc_start: 0.9121 (mmp) cc_final: 0.8702 (mmm) REVERT: e 416 MET cc_start: 0.8039 (ptt) cc_final: 0.6955 (ptt) REVERT: A 339 MET cc_start: 0.6522 (mmt) cc_final: 0.5600 (mpp) REVERT: V 142 MET cc_start: 0.8246 (pmm) cc_final: 0.8045 (pmm) REVERT: V 236 ASP cc_start: 0.8306 (m-30) cc_final: 0.7779 (p0) REVERT: W 26 ARG cc_start: 0.9690 (tpt90) cc_final: 0.8966 (tpt90) REVERT: W 30 MET cc_start: 0.9117 (ptp) cc_final: 0.8876 (ptm) REVERT: X 315 MET cc_start: 0.8929 (tpp) cc_final: 0.8509 (mmm) REVERT: X 515 MET cc_start: 0.8728 (pmm) cc_final: 0.8162 (pmm) REVERT: X 681 MET cc_start: 0.8618 (pmm) cc_final: 0.8079 (pmm) REVERT: X 1119 MET cc_start: 0.8305 (tpp) cc_final: 0.8095 (tpp) REVERT: Y 166 LEU cc_start: 0.9499 (tp) cc_final: 0.9259 (pp) REVERT: Y 237 MET cc_start: 0.8789 (ttt) cc_final: 0.8438 (tpt) REVERT: Y 1145 PHE cc_start: 0.8542 (m-80) cc_final: 0.7833 (m-80) REVERT: Y 1260 MET cc_start: 0.8034 (tpt) cc_final: 0.7534 (tpp) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.6640 time to fit residues: 282.4440 Evaluate side-chains 234 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 6.032 ------------------------------------------------------------------------------- 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: 4.9990 chunk 120 optimal weight: 1.9990 chunk 359 optimal weight: 3.9990 chunk 151 optimal weight: 20.0000 chunk 612 optimal weight: 8.9990 chunk 508 optimal weight: 20.0000 chunk 283 optimal weight: 0.8980 chunk 50 optimal weight: 20.0000 chunk 202 optimal weight: 7.9990 chunk 321 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 172 GLN ** a 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 37 HIS ** 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 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** X1157 GLN X1209 GLN ** 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 52481 Z= 0.206 Angle : 0.583 12.178 71226 Z= 0.292 Chirality : 0.041 0.234 8152 Planarity : 0.004 0.097 8987 Dihedral : 13.065 174.170 8057 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 21.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.04 % Allowed : 2.27 % Favored : 97.69 % 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: -1.10 (0.11), residues: 6289 helix: 0.58 (0.11), residues: 2327 sheet: -1.44 (0.17), residues: 869 loop : -1.53 (0.11), residues: 3093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP V 321 HIS 0.006 0.001 HIS Y 777 PHE 0.021 0.001 PHE f 412 TYR 0.032 0.001 TYR Y 269 ARG 0.008 0.000 ARG f 221 *********************** 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 255 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 253 time to evaluate : 6.561 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: f 219 MET cc_start: 0.8632 (mmp) cc_final: 0.8373 (mmm) REVERT: a 1 MET cc_start: 0.8285 (pmm) cc_final: 0.8079 (pmm) REVERT: a 29 MET cc_start: 0.2894 (ptt) cc_final: 0.1730 (ptp) REVERT: a 245 MET cc_start: 0.8560 (mmm) cc_final: 0.8069 (mmm) REVERT: a 341 MET cc_start: 0.8045 (tmm) cc_final: 0.7494 (tmm) REVERT: a 343 LEU cc_start: 0.8853 (mt) cc_final: 0.8594 (mt) REVERT: b 1 MET cc_start: 0.8503 (ppp) cc_final: 0.8215 (ppp) REVERT: b 29 MET cc_start: 0.8279 (ptm) cc_final: 0.7619 (ptt) REVERT: b 380 MET cc_start: 0.9102 (mtm) cc_final: 0.8554 (ptp) REVERT: c 327 MET cc_start: 0.8130 (mmm) cc_final: 0.7653 (mmt) REVERT: c 380 MET cc_start: 0.8999 (mtm) cc_final: 0.8634 (mtp) REVERT: d 219 MET cc_start: 0.7909 (mmp) cc_final: 0.7264 (mmm) REVERT: e 147 MET cc_start: 0.8718 (mmp) cc_final: 0.8511 (mmm) REVERT: e 416 MET cc_start: 0.8054 (ptt) cc_final: 0.6963 (ptt) REVERT: A 339 MET cc_start: 0.6684 (mmt) cc_final: 0.5778 (mpp) REVERT: U 51 MET cc_start: 0.8618 (mmp) cc_final: 0.8379 (mmm) REVERT: V 236 ASP cc_start: 0.8297 (m-30) cc_final: 0.7854 (p0) REVERT: W 26 ARG cc_start: 0.9683 (tpt90) cc_final: 0.8997 (tpt90) REVERT: W 30 MET cc_start: 0.9158 (ptp) cc_final: 0.8934 (ptm) REVERT: X 315 MET cc_start: 0.8951 (tpp) cc_final: 0.8558 (mmm) REVERT: X 515 MET cc_start: 0.8613 (pmm) cc_final: 0.8341 (pmm) REVERT: X 681 MET cc_start: 0.8650 (pmm) cc_final: 0.8144 (pmm) REVERT: Y 166 LEU cc_start: 0.9503 (tp) cc_final: 0.9288 (pp) REVERT: Y 192 MET cc_start: 0.7640 (mmm) cc_final: 0.7079 (mmm) REVERT: Y 484 MET cc_start: 0.7819 (mmp) cc_final: 0.7455 (mmm) REVERT: Y 1145 PHE cc_start: 0.8539 (m-80) cc_final: 0.7802 (m-80) REVERT: Y 1260 MET cc_start: 0.8027 (tpt) cc_final: 0.7569 (tpp) outliers start: 2 outliers final: 1 residues processed: 255 average time/residue: 0.6356 time to fit residues: 276.4577 Evaluate side-chains 235 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 234 time to evaluate : 5.673 ------------------------------------------------------------------------------- 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: 9.9990 chunk 69 optimal weight: 6.9990 chunk 348 optimal weight: 30.0000 chunk 447 optimal weight: 0.7980 chunk 346 optimal weight: 8.9990 chunk 515 optimal weight: 50.0000 chunk 341 optimal weight: 0.0000 chunk 610 optimal weight: 7.9990 chunk 381 optimal weight: 9.9990 chunk 371 optimal weight: 1.9990 chunk 281 optimal weight: 0.0370 overall best weight: 1.9666 ------------------------------------------------------------------------------- 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 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 72 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.4886 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 : 0.558 10.130 71226 Z= 0.279 Chirality : 0.041 0.231 8152 Planarity : 0.004 0.094 8987 Dihedral : 12.944 173.995 8057 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % 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: -0.90 (0.11), residues: 6289 helix: 0.74 (0.11), residues: 2312 sheet: -1.29 (0.17), residues: 848 loop : -1.42 (0.11), residues: 3129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP X1276 HIS 0.005 0.001 HIS Y 777 PHE 0.025 0.001 PHE b 413 TYR 0.030 0.001 TYR Y 269 ARG 0.007 0.000 ARG f 221 *********************** 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 253 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 5.957 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: f 219 MET cc_start: 0.8628 (mmp) cc_final: 0.8367 (mmm) REVERT: a 29 MET cc_start: 0.2814 (ptt) cc_final: 0.1626 (ptp) REVERT: a 245 MET cc_start: 0.8512 (mmm) cc_final: 0.8069 (mmm) REVERT: a 341 MET cc_start: 0.8061 (tmm) cc_final: 0.7489 (tmm) REVERT: a 343 LEU cc_start: 0.8912 (mt) cc_final: 0.8659 (mt) REVERT: b 1 MET cc_start: 0.8509 (ppp) cc_final: 0.8202 (ppp) REVERT: b 186 MET cc_start: 0.8058 (pmm) cc_final: 0.7690 (pmm) REVERT: b 380 MET cc_start: 0.9014 (mtm) cc_final: 0.8395 (ptp) REVERT: b 390 MET cc_start: 0.8208 (ppp) cc_final: 0.7634 (ppp) REVERT: c 21 MET cc_start: 0.8133 (mtt) cc_final: 0.7827 (mtp) REVERT: c 29 MET cc_start: 0.8549 (ptm) cc_final: 0.8309 (ptt) REVERT: c 219 MET cc_start: 0.8292 (mmm) cc_final: 0.7916 (mmm) REVERT: c 327 MET cc_start: 0.8215 (mmm) cc_final: 0.7711 (mmt) REVERT: d 29 MET cc_start: 0.6702 (pmm) cc_final: 0.6489 (pmm) REVERT: d 219 MET cc_start: 0.7911 (mmp) cc_final: 0.7265 (mmm) REVERT: e 186 MET cc_start: 0.8746 (pmm) cc_final: 0.8471 (pmm) REVERT: e 396 MET cc_start: 0.9236 (mmp) cc_final: 0.8772 (mmm) REVERT: e 416 MET cc_start: 0.7888 (ptt) cc_final: 0.6765 (ptt) REVERT: A 339 MET cc_start: 0.6602 (mmt) cc_final: 0.5728 (mpp) REVERT: V 236 ASP cc_start: 0.8181 (m-30) cc_final: 0.7786 (p0) REVERT: W 26 ARG cc_start: 0.9583 (tpt90) cc_final: 0.8916 (tpt90) REVERT: X 315 MET cc_start: 0.8962 (tpp) cc_final: 0.8618 (mmm) REVERT: X 515 MET cc_start: 0.8583 (pmm) cc_final: 0.8302 (pmm) REVERT: X 681 MET cc_start: 0.8573 (pmm) cc_final: 0.8097 (pmm) REVERT: X 1119 MET cc_start: 0.8180 (tpp) cc_final: 0.7913 (tpp) REVERT: X 1304 MET cc_start: 0.8575 (mmm) cc_final: 0.8272 (mmm) REVERT: Y 151 MET cc_start: 0.4026 (pmm) cc_final: 0.3692 (pmm) REVERT: Y 166 LEU cc_start: 0.9532 (tp) cc_final: 0.9322 (pp) REVERT: Y 192 MET cc_start: 0.7756 (mmm) cc_final: 0.7186 (mmm) REVERT: Y 484 MET cc_start: 0.7793 (mmp) cc_final: 0.7440 (mmm) REVERT: Y 1145 PHE cc_start: 0.8525 (m-80) cc_final: 0.7840 (m-80) REVERT: Y 1260 MET cc_start: 0.7955 (tpt) cc_final: 0.7486 (tpp) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.6499 time to fit residues: 280.9804 Evaluate side-chains 233 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 6.209 ------------------------------------------------------------------------------- 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: 5.9990 chunk 243 optimal weight: 10.0000 chunk 364 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 387 optimal weight: 30.0000 chunk 415 optimal weight: 10.0000 chunk 301 optimal weight: 0.0040 chunk 56 optimal weight: 30.0000 chunk 479 optimal weight: 8.9990 overall best weight: 5.2000 ------------------------------------------------------------------------------- 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 172 GLN ** a 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 70 GLN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 208 ASN ** X 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 235 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** X 965 GLN ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1157 GLN X1209 GLN ** 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 477 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.5396 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= 0.256 Angle : 0.624 12.001 71226 Z= 0.315 Chirality : 0.041 0.225 8152 Planarity : 0.004 0.097 8987 Dihedral : 13.057 173.543 8057 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 24.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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: -0.99 (0.11), residues: 6289 helix: 0.60 (0.11), residues: 2330 sheet: -1.29 (0.17), residues: 864 loop : -1.44 (0.11), residues: 3095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP X 183 HIS 0.008 0.001 HIS Y 777 PHE 0.017 0.001 PHE a 412 TYR 0.027 0.002 TYR Y 269 ARG 0.008 0.000 ARG f 221 *********************** 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 254 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 5.769 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: f 21 MET cc_start: -0.5103 (mmt) cc_final: -0.6428 (tpt) REVERT: f 219 MET cc_start: 0.8614 (mmp) cc_final: 0.8337 (mmm) REVERT: a 29 MET cc_start: 0.2897 (ptt) cc_final: 0.1618 (ptp) REVERT: a 245 MET cc_start: 0.8579 (mmm) cc_final: 0.8062 (mmm) REVERT: a 343 LEU cc_start: 0.8898 (mt) cc_final: 0.8629 (mt) REVERT: b 1 MET cc_start: 0.8608 (ppp) cc_final: 0.8338 (ppp) REVERT: b 186 MET cc_start: 0.8094 (pmm) cc_final: 0.7702 (pmm) REVERT: b 380 MET cc_start: 0.9020 (mtm) cc_final: 0.8553 (mtp) REVERT: b 390 MET cc_start: 0.8414 (ppp) cc_final: 0.7853 (ppp) REVERT: c 327 MET cc_start: 0.8238 (mmm) cc_final: 0.7724 (mmt) REVERT: c 380 MET cc_start: 0.9002 (mtm) cc_final: 0.8597 (mtp) REVERT: d 219 MET cc_start: 0.8167 (mmp) cc_final: 0.7458 (mmm) REVERT: d 396 MET cc_start: 0.9050 (mmp) cc_final: 0.8779 (mmm) REVERT: e 21 MET cc_start: 0.8681 (ttt) cc_final: 0.8455 (ttt) REVERT: e 390 MET cc_start: 0.9307 (pmm) cc_final: 0.8967 (pmm) REVERT: e 396 MET cc_start: 0.9262 (mmp) cc_final: 0.8984 (mmm) REVERT: e 416 MET cc_start: 0.7994 (ptt) cc_final: 0.6888 (ptt) REVERT: A 339 MET cc_start: 0.6566 (mmt) cc_final: 0.5695 (mpp) REVERT: A 361 LYS cc_start: 0.8279 (mmtt) cc_final: 0.8056 (mptt) REVERT: V 236 ASP cc_start: 0.8239 (m-30) cc_final: 0.7801 (p0) REVERT: W 26 ARG cc_start: 0.9643 (tpt90) cc_final: 0.9014 (tpt90) REVERT: W 30 MET cc_start: 0.8922 (ptp) cc_final: 0.8688 (ptm) REVERT: X 315 MET cc_start: 0.8973 (tpp) cc_final: 0.8495 (mmm) REVERT: X 515 MET cc_start: 0.8802 (pmm) cc_final: 0.8293 (pmm) REVERT: X 681 MET cc_start: 0.8682 (pmm) cc_final: 0.8151 (pmm) REVERT: X 1119 MET cc_start: 0.8306 (tpp) cc_final: 0.8083 (tpp) REVERT: Y 192 MET cc_start: 0.7722 (mmm) cc_final: 0.7438 (mmm) REVERT: Y 237 MET cc_start: 0.8561 (ttm) cc_final: 0.8262 (tpp) REVERT: Y 298 MET cc_start: 0.4213 (ttt) cc_final: 0.3076 (ppp) REVERT: Y 484 MET cc_start: 0.7983 (mmp) cc_final: 0.7715 (mmm) REVERT: Y 1145 PHE cc_start: 0.8697 (m-80) cc_final: 0.8090 (m-80) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.6593 time to fit residues: 286.1811 Evaluate side-chains 232 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 5.710 ------------------------------------------------------------------------------- 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: 0.9980 chunk 584 optimal weight: 3.9990 chunk 533 optimal weight: 3.9990 chunk 568 optimal weight: 8.9990 chunk 342 optimal weight: 9.9990 chunk 247 optimal weight: 0.6980 chunk 446 optimal weight: 0.0470 chunk 174 optimal weight: 10.0000 chunk 513 optimal weight: 0.9990 chunk 537 optimal weight: 2.9990 chunk 566 optimal weight: 5.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- 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 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 256 HIS ** d 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 70 GLN ** A 316 GLN ** 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 X 799 ASN ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1157 GLN X1209 GLN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 52481 Z= 0.147 Angle : 0.575 11.219 71226 Z= 0.285 Chirality : 0.041 0.230 8152 Planarity : 0.004 0.121 8987 Dihedral : 12.866 173.747 8057 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.18 % Favored : 95.80 % Rotamer: Outliers : 0.02 % Allowed : 0.45 % Favored : 99.54 % 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: -0.73 (0.11), residues: 6289 helix: 0.85 (0.11), residues: 2292 sheet: -1.12 (0.18), residues: 837 loop : -1.32 (0.11), residues: 3160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Y 409 HIS 0.004 0.001 HIS c 42 PHE 0.019 0.001 PHE a 412 TYR 0.030 0.001 TYR Y 269 ARG 0.007 0.000 ARG Y 278 *********************** 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 255 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 254 time to evaluate : 5.931 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: f 21 MET cc_start: -0.5454 (mmt) cc_final: -0.6632 (tpt) REVERT: f 219 MET cc_start: 0.8502 (mmp) cc_final: 0.8260 (mmm) REVERT: a 29 MET cc_start: 0.3126 (ptt) cc_final: 0.2065 (ptp) REVERT: a 245 MET cc_start: 0.8479 (mmm) cc_final: 0.8019 (mmm) REVERT: a 341 MET cc_start: 0.8041 (tmm) cc_final: 0.7504 (tmm) REVERT: a 343 LEU cc_start: 0.8938 (mt) cc_final: 0.8674 (mt) REVERT: b 1 MET cc_start: 0.8441 (ppp) cc_final: 0.8183 (ppp) REVERT: b 29 MET cc_start: 0.7747 (pmm) cc_final: 0.7175 (pmm) REVERT: b 219 MET cc_start: 0.8694 (mmm) cc_final: 0.8311 (mmm) REVERT: b 390 MET cc_start: 0.8200 (ppp) cc_final: 0.7605 (ppp) REVERT: c 21 MET cc_start: 0.8216 (mtt) cc_final: 0.7952 (mtp) REVERT: c 29 MET cc_start: 0.7506 (ptt) cc_final: 0.7117 (ptt) REVERT: c 219 MET cc_start: 0.8261 (mmm) cc_final: 0.7912 (mmm) REVERT: c 327 MET cc_start: 0.8186 (mmm) cc_final: 0.7692 (mmt) REVERT: c 380 MET cc_start: 0.8969 (mtm) cc_final: 0.8577 (mtm) REVERT: d 219 MET cc_start: 0.7979 (mmp) cc_final: 0.7322 (mmm) REVERT: d 396 MET cc_start: 0.8960 (mmp) cc_final: 0.8728 (mmm) REVERT: e 390 MET cc_start: 0.9362 (pmm) cc_final: 0.9027 (pmm) REVERT: e 396 MET cc_start: 0.9208 (mmp) cc_final: 0.8892 (mmm) REVERT: e 416 MET cc_start: 0.7938 (ptt) cc_final: 0.6777 (ptt) REVERT: A 339 MET cc_start: 0.6605 (mmt) cc_final: 0.5769 (mpp) REVERT: A 361 LYS cc_start: 0.8262 (mmtt) cc_final: 0.8029 (mptt) REVERT: V 236 ASP cc_start: 0.8159 (m-30) cc_final: 0.7834 (p0) REVERT: W 26 ARG cc_start: 0.9629 (tpt90) cc_final: 0.8872 (tpm170) REVERT: X 369 MET cc_start: 0.8896 (tmm) cc_final: 0.8477 (tmm) REVERT: X 515 MET cc_start: 0.8583 (pmm) cc_final: 0.8284 (pmm) REVERT: X 1119 MET cc_start: 0.8169 (tpp) cc_final: 0.7965 (tpp) REVERT: Y 237 MET cc_start: 0.8503 (ttm) cc_final: 0.8185 (tpp) REVERT: Y 484 MET cc_start: 0.7679 (mmp) cc_final: 0.7374 (mmm) REVERT: Y 1145 PHE cc_start: 0.8499 (m-80) cc_final: 0.7961 (m-80) REVERT: Y 1260 MET cc_start: 0.7983 (tpt) cc_final: 0.7653 (tpp) outliers start: 1 outliers final: 0 residues processed: 255 average time/residue: 0.6576 time to fit residues: 286.6333 Evaluate side-chains 233 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 6.372 ------------------------------------------------------------------------------- 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: 0.9990 chunk 601 optimal weight: 0.9990 chunk 366 optimal weight: 5.9990 chunk 285 optimal weight: 0.0970 chunk 417 optimal weight: 6.9990 chunk 630 optimal weight: 30.0000 chunk 580 optimal weight: 7.9990 chunk 502 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 387 optimal weight: 8.9990 chunk 307 optimal weight: 5.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** 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 235 ASN ** 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 799 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 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.5399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 52481 Z= 0.165 Angle : 0.567 9.991 71226 Z= 0.282 Chirality : 0.041 0.243 8152 Planarity : 0.004 0.094 8987 Dihedral : 12.819 173.977 8057 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: -0.71 (0.11), residues: 6289 helix: 0.85 (0.11), residues: 2339 sheet: -1.06 (0.17), residues: 853 loop : -1.34 (0.11), residues: 3097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y1193 HIS 0.005 0.001 HIS Y 777 PHE 0.018 0.001 PHE a 412 TYR 0.030 0.001 TYR Y 269 ARG 0.009 0.000 ARG Y 278 ********************** 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 249 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 6.262 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: f 21 MET cc_start: -0.5371 (mmt) cc_final: -0.6527 (tpt) REVERT: f 219 MET cc_start: 0.8460 (mmp) cc_final: 0.8258 (mmm) REVERT: a 29 MET cc_start: 0.1972 (ptt) cc_final: 0.0927 (ptp) REVERT: a 245 MET cc_start: 0.8512 (mmm) cc_final: 0.8036 (mmm) REVERT: a 341 MET cc_start: 0.8090 (tmm) cc_final: 0.7567 (tmm) REVERT: a 343 LEU cc_start: 0.8924 (mt) cc_final: 0.8670 (mt) REVERT: b 1 MET cc_start: 0.8439 (ppp) cc_final: 0.8188 (ppp) REVERT: b 29 MET cc_start: 0.7929 (pmm) cc_final: 0.7331 (pmm) REVERT: b 186 MET cc_start: 0.7951 (pmm) cc_final: 0.7611 (pmm) REVERT: b 219 MET cc_start: 0.8716 (mmm) cc_final: 0.8322 (mmm) REVERT: b 380 MET cc_start: 0.8999 (mtm) cc_final: 0.8389 (ptp) REVERT: b 390 MET cc_start: 0.8211 (ppp) cc_final: 0.7603 (ppp) REVERT: c 21 MET cc_start: 0.8568 (mtt) cc_final: 0.7518 (mmt) REVERT: c 29 MET cc_start: 0.7348 (ptt) cc_final: 0.6850 (ptt) REVERT: c 219 MET cc_start: 0.8295 (mmm) cc_final: 0.7931 (mmm) REVERT: c 327 MET cc_start: 0.8194 (mmm) cc_final: 0.7705 (mmt) REVERT: d 219 MET cc_start: 0.7998 (mmp) cc_final: 0.7344 (mmm) REVERT: d 390 MET cc_start: 0.8760 (pmm) cc_final: 0.8362 (pmm) REVERT: d 396 MET cc_start: 0.9026 (mmp) cc_final: 0.8786 (mmm) REVERT: e 186 MET cc_start: 0.8465 (pmm) cc_final: 0.8136 (pmm) REVERT: e 390 MET cc_start: 0.9252 (pmm) cc_final: 0.8892 (pmm) REVERT: e 396 MET cc_start: 0.9229 (mmp) cc_final: 0.8758 (mmm) REVERT: e 416 MET cc_start: 0.7916 (ptt) cc_final: 0.6786 (ptt) REVERT: A 339 MET cc_start: 0.6638 (mmt) cc_final: 0.5789 (mpp) REVERT: A 361 LYS cc_start: 0.8282 (mmtt) cc_final: 0.8048 (mptt) REVERT: V 236 ASP cc_start: 0.8151 (m-30) cc_final: 0.7844 (p0) REVERT: W 26 ARG cc_start: 0.9575 (tpt90) cc_final: 0.9102 (tpm170) REVERT: X 369 MET cc_start: 0.8822 (tmm) cc_final: 0.8352 (tmm) REVERT: X 515 MET cc_start: 0.8709 (pmm) cc_final: 0.8380 (pmm) REVERT: X 1273 MET cc_start: 0.8127 (ttp) cc_final: 0.7554 (ttp) REVERT: Y 192 MET cc_start: 0.7602 (mmm) cc_final: 0.7261 (mmm) REVERT: Y 484 MET cc_start: 0.7862 (mmp) cc_final: 0.7562 (mmm) REVERT: Y 1145 PHE cc_start: 0.8479 (m-80) cc_final: 0.7921 (m-80) REVERT: Y 1260 MET cc_start: 0.7950 (tpt) cc_final: 0.7560 (tpp) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.6578 time to fit residues: 280.9797 Evaluate side-chains 230 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 5.875 ------------------------------------------------------------------------------- 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: 9.9990 chunk 534 optimal weight: 20.0000 chunk 153 optimal weight: 0.9980 chunk 463 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 502 optimal weight: 9.9990 chunk 210 optimal weight: 20.0000 chunk 516 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 overall best weight: 6.5988 ------------------------------------------------------------------------------- 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 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 344 HIS ** d 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 70 GLN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 147 GLN ** W 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 235 ASN ** 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 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 965 GLN ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1209 GLN X1257 GLN ** Y 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 489 ASN Y 702 GLN Y 805 GLN ** Y 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1295 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.035114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.022145 restraints weight = 763961.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.022492 restraints weight = 503678.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.022847 restraints weight = 379093.906| |-----------------------------------------------------------------------------| r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.5979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 52481 Z= 0.306 Angle : 0.679 14.654 71226 Z= 0.342 Chirality : 0.042 0.235 8152 Planarity : 0.005 0.101 8987 Dihedral : 13.060 173.523 8057 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 27.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.19 % Favored : 93.80 % Rotamer: Outliers : 0.02 % Allowed : 0.41 % Favored : 99.57 % 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: -0.95 (0.11), residues: 6289 helix: 0.57 (0.11), residues: 2357 sheet: -1.23 (0.17), residues: 867 loop : -1.38 (0.11), residues: 3065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP X 183 HIS 0.009 0.001 HIS Y 777 PHE 0.027 0.002 PHE Y 116 TYR 0.031 0.002 TYR Y 269 ARG 0.014 0.001 ARG Y 278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8680.46 seconds wall clock time: 161 minutes 37.91 seconds (9697.91 seconds total)