Starting phenix.real_space_refine on Tue Nov 21 18:58:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x75_33032/11_2023/7x75_33032.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x75_33032/11_2023/7x75_33032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x75_33032/11_2023/7x75_33032.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x75_33032/11_2023/7x75_33032.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x75_33032/11_2023/7x75_33032.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x75_33032/11_2023/7x75_33032.pdb" } resolution = 3.45 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= 0.045 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: 7 Type Number sf(0) Gaussians Zn 20 6.06 5 P 168 5.49 5 Mg 1 5.21 5 S 126 5.16 5 C 21252 2.51 5 N 6265 2.21 5 O 7040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A GLU 88": "OE1" <-> "OE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C GLU 101": "OE1" <-> "OE2" Residue "C GLU 203": "OE1" <-> "OE2" Residue "C GLU 383": "OE1" <-> "OE2" Residue "C GLU 396": "OE1" <-> "OE2" Residue "C GLU 415": "OE1" <-> "OE2" Residue "C GLU 457": "OE1" <-> "OE2" Residue "C GLU 499": "OE1" <-> "OE2" Residue "C GLU 684": "OE1" <-> "OE2" Residue "C GLU 695": "OE1" <-> "OE2" Residue "C GLU 742": "OE1" <-> "OE2" Residue "C GLU 765": "OE1" <-> "OE2" Residue "C GLU 772": "OE1" <-> "OE2" Residue "C GLU 804": "OE1" <-> "OE2" Residue "C GLU 813": "OE1" <-> "OE2" Residue "C GLU 967": "OE1" <-> "OE2" Residue "C GLU 969": "OE1" <-> "OE2" Residue "C GLU 984": "OE1" <-> "OE2" Residue "C GLU 1002": "OE1" <-> "OE2" Residue "D GLU 9": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D GLU 364": "OE1" <-> "OE2" Residue "D GLU 493": "OE1" <-> "OE2" Residue "D GLU 593": "OE1" <-> "OE2" Residue "D GLU 682": "OE1" <-> "OE2" Residue "D GLU 952": "OE1" <-> "OE2" Residue "D GLU 953": "OE1" <-> "OE2" Residue "D GLU 999": "OE1" <-> "OE2" Residue "D GLU 1152": "OE1" <-> "OE2" Residue "F GLU 233": "OE1" <-> "OE2" Residue "F GLU 235": "OE1" <-> "OE2" Residue "F GLU 306": "OE1" <-> "OE2" Residue "F GLU 357": "OE1" <-> "OE2" Residue "F GLU 380": "OE1" <-> "OE2" Residue "F GLU 417": "OE1" <-> "OE2" Residue "F GLU 454": "OE1" <-> "OE2" Residue "F GLU 474": "OE1" <-> "OE2" Residue "F GLU 490": "OE1" <-> "OE2" Residue "H GLU 63": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 34872 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1742 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 13, 'TRANS': 212} Chain: "B" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1792 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 13, 'TRANS': 219} Chain: "C" Number of atoms: 8692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1116, 8692 Classifications: {'peptide': 1116} Link IDs: {'PTRANS': 58, 'TRANS': 1057} Chain: "D" Number of atoms: 9846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1259, 9846 Classifications: {'peptide': 1259} Link IDs: {'PTRANS': 56, 'TRANS': 1202} Chain: "E" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 597 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "F" Number of atoms: 2396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2396 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 288} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "H" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "K" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "L" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "M" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "N" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "O" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1714 Classifications: {'DNA': 84} Link IDs: {'rna3p': 83} Chain: "S" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "P" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1730 Classifications: {'DNA': 84} Link IDs: {'rna3p': 83} Chain: "D" 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: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12673 SG CYS D 60 70.811 109.205 112.275 1.00 69.88 S ATOM 12691 SG CYS D 62 69.812 110.590 115.538 1.00 77.34 S ATOM 12800 SG CYS D 75 73.632 110.140 114.908 1.00 78.06 S ATOM 12826 SG CYS D 78 71.661 107.268 115.513 1.00 70.79 S ATOM 19225 SG CYS D 886 110.141 61.388 84.195 1.00 68.68 S ATOM 19789 SG CYS D 962 106.742 61.472 85.616 1.00 58.06 S ATOM 19837 SG CYS D 969 107.117 62.924 82.086 1.00 48.20 S ATOM 19856 SG CYS D 972 107.243 59.327 82.557 1.00 51.55 S ATOM 25721 SG CYS G 90 60.544 186.295 77.538 1.00151.17 S ATOM 25743 SG CYS G 93 58.009 187.154 74.858 1.00151.76 S ATOM 26016 SG CYS G 130 58.272 188.890 78.433 1.00148.17 S ATOM 26035 SG CYS G 133 56.616 185.557 77.922 1.00145.54 S ATOM 25635 SG CYS G 79 73.073 195.180 74.893 1.00156.90 S ATOM 26705 SG CYS H 90 92.044 179.962 92.468 1.00152.25 S ATOM 26727 SG CYS H 93 94.353 177.963 94.695 1.00152.19 S ATOM 27000 SG CYS H 130 93.317 181.547 95.638 1.00151.24 S ATOM 27019 SG CYS H 133 95.887 180.649 92.785 1.00148.20 S ATOM 26619 SG CYS H 79 77.112 174.673 98.346 1.00146.86 S ATOM 27689 SG CYS K 90 123.927 185.058 53.705 1.00147.97 S ATOM 27711 SG CYS K 93 124.337 181.621 52.609 1.00147.71 S ATOM 27984 SG CYS K 130 127.134 183.328 54.686 1.00149.28 S ATOM 28003 SG CYS K 133 126.497 183.773 50.798 1.00144.47 S ATOM 27603 SG CYS K 79 115.395 183.780 67.107 1.00154.91 S ATOM 28673 SG CYS L 90 102.905 210.620 66.809 1.00144.73 S ATOM 28695 SG CYS L 93 101.310 213.960 67.147 1.00143.14 S ATOM 28968 SG CYS L 130 103.458 212.752 70.075 1.00148.05 S ATOM 28987 SG CYS L 133 100.077 211.151 69.311 1.00145.74 S ATOM 28587 SG CYS L 79 115.832 213.015 55.960 1.00153.69 S ATOM 29657 SG CYS M 90 65.428 172.892 34.927 1.00151.94 S ATOM 29679 SG CYS M 93 61.910 173.510 36.440 1.00146.63 S ATOM 29952 SG CYS M 130 62.364 171.558 33.199 1.00149.24 S ATOM 29971 SG CYS M 133 62.941 175.353 33.376 1.00144.40 S ATOM 29571 SG CYS M 79 67.748 158.586 41.585 1.00156.09 S ATOM 30641 SG CYS N 90 95.360 155.557 35.537 1.00143.45 S ATOM 30663 SG CYS N 93 99.203 155.372 35.650 1.00141.51 S ATOM 30936 SG CYS N 130 97.192 153.747 32.826 1.00141.95 S ATOM 30955 SG CYS N 133 97.203 152.279 36.340 1.00137.43 S ATOM 30555 SG CYS N 79 93.075 166.763 24.850 1.00151.94 S Time building chain proxies: 17.46, per 1000 atoms: 0.50 Number of scatterers: 34872 At special positions: 0 Unit cell: (142.8, 229.95, 200.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 20 29.99 S 126 16.00 P 168 15.00 Mg 1 11.99 O 7040 8.00 N 6265 7.00 C 21252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.35 Conformation dependent library (CDL) restraints added in 5.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1402 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 78 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 62 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 75 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 60 " pdb=" ZN D1403 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 962 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 972 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 969 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 886 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 130 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 90 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 93 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 133 " pdb=" ZN G 202 " pdb="ZN ZN G 202 " - pdb=" NE2 HIS G 85 " pdb="ZN ZN G 202 " - pdb=" NE2 HIS G 87 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 79 " pdb=" ZN G 203 " pdb="ZN ZN G 203 " - pdb=" NE2 HIS G 86 " pdb="ZN ZN G 203 " - pdb=" NE2 HIS G 84 " pdb="ZN ZN G 203 " - pdb=" NE2 HIS G 122 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 93 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 90 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 133 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 130 " pdb=" ZN H 202 " pdb="ZN ZN H 202 " - pdb=" NE2 HIS H 85 " pdb="ZN ZN H 202 " - pdb=" NE2 HIS H 87 " pdb="ZN ZN H 202 " - pdb=" SG CYS H 79 " pdb=" ZN H 203 " pdb="ZN ZN H 203 " - pdb=" NE2 HIS H 86 " pdb="ZN ZN H 203 " - pdb=" NE2 HIS H 84 " pdb="ZN ZN H 203 " - pdb=" NE2 HIS H 122 " pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 93 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 90 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 130 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 133 " pdb=" ZN K 202 " pdb="ZN ZN K 202 " - pdb=" NE2 HIS K 85 " pdb="ZN ZN K 202 " - pdb=" SG CYS K 79 " pdb="ZN ZN K 202 " - pdb=" NE2 HIS K 87 " pdb=" ZN K 203 " pdb="ZN ZN K 203 " - pdb=" NE2 HIS K 122 " pdb="ZN ZN K 203 " - pdb=" NE2 HIS K 86 " pdb="ZN ZN K 203 " - pdb=" NE2 HIS K 84 " pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 93 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 133 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 90 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 130 " pdb=" ZN L 202 " pdb="ZN ZN L 202 " - pdb=" NE2 HIS L 85 " pdb="ZN ZN L 202 " - pdb=" NE2 HIS L 87 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 79 " pdb=" ZN L 203 " pdb="ZN ZN L 203 " - pdb=" NE2 HIS L 86 " pdb="ZN ZN L 203 " - pdb=" NE2 HIS L 84 " pdb="ZN ZN L 203 " - pdb=" NE2 HIS L 122 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 133 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 93 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 130 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 90 " pdb=" ZN M 202 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 79 " pdb="ZN ZN M 202 " - pdb=" NE2 HIS M 87 " pdb="ZN ZN M 202 " - pdb=" NE2 HIS M 85 " pdb=" ZN M 203 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 122 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 84 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 86 " pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 130 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 133 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 90 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 93 " pdb=" ZN N 202 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 79 " pdb="ZN ZN N 202 " - pdb=" NE2 HIS N 85 " pdb="ZN ZN N 202 " - pdb=" NE2 HIS N 87 " pdb=" ZN N 203 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 122 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 86 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 84 " Number of angles added : 48 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7468 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 47 sheets defined 44.9% alpha, 14.4% beta 62 base pairs and 125 stacking pairs defined. Time for finding SS restraints: 13.09 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 Processing helix chain 'A' and resid 72 through 82 removed outlier: 3.764A pdb=" N GLN A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 225 Processing helix chain 'B' and resid 30 through 45 Processing helix chain 'B' and resid 72 through 83 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 203 through 221 Processing helix chain 'B' and resid 222 through 226 Processing helix chain 'C' and resid 38 through 50 removed outlier: 3.705A pdb=" N SER C 44 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 65 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 106 through 114 Processing helix chain 'C' and resid 221 through 229 removed outlier: 4.173A pdb=" N LEU C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 241 Processing helix chain 'C' and resid 243 through 253 Processing helix chain 'C' and resid 257 through 270 Processing helix chain 'C' and resid 276 through 288 Processing helix chain 'C' and resid 297 through 309 removed outlier: 3.569A pdb=" N LYS C 306 " --> pdb=" O TYR C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 337 Processing helix chain 'C' and resid 366 through 392 Processing helix chain 'C' and resid 399 through 404 removed outlier: 3.655A pdb=" N ILE C 404 " --> pdb=" O PRO C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 418 removed outlier: 3.741A pdb=" N PHE C 417 " --> pdb=" O ILE C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 439 Processing helix chain 'C' and resid 455 through 460 removed outlier: 3.627A pdb=" N ARG C 459 " --> pdb=" O GLY C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 removed outlier: 4.024A pdb=" N ARG C 524 " --> pdb=" O ASP C 520 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE C 525 " --> pdb=" O GLU C 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 525' Processing helix chain 'C' and resid 549 through 553 removed outlier: 3.536A pdb=" N GLU C 553 " --> pdb=" O ARG C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 580 Processing helix chain 'C' and resid 587 through 598 Processing helix chain 'C' and resid 616 through 624 Processing helix chain 'C' and resid 716 through 720 removed outlier: 4.334A pdb=" N ASP C 719 " --> pdb=" O ASN C 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 730 Processing helix chain 'C' and resid 801 through 812 Processing helix chain 'C' and resid 906 through 912 removed outlier: 3.953A pdb=" N SER C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 928 Processing helix chain 'C' and resid 937 through 947 Processing helix chain 'C' and resid 966 through 976 Processing helix chain 'C' and resid 1021 through 1026 removed outlier: 3.587A pdb=" N LYS C1025 " --> pdb=" O LEU C1021 " (cutoff:3.500A) Processing helix chain 'C' and resid 1054 through 1065 Processing helix chain 'C' and resid 1066 through 1075 removed outlier: 3.755A pdb=" N LEU C1070 " --> pdb=" O ALA C1066 " (cutoff:3.500A) Processing helix chain 'C' and resid 1080 through 1094 removed outlier: 4.171A pdb=" N VAL C1085 " --> pdb=" O VAL C1081 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS C1086 " --> pdb=" O THR C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1103 through 1115 removed outlier: 3.787A pdb=" N LYS C1107 " --> pdb=" O PRO C1103 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 86 through 91 removed outlier: 3.790A pdb=" N GLU D 90 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 130 removed outlier: 3.776A pdb=" N TYR D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'D' and resid 147 through 188 Processing helix chain 'D' and resid 192 through 227 removed outlier: 3.775A pdb=" N LYS D 196 " --> pdb=" O ASP D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 removed outlier: 3.641A pdb=" N PHE D 248 " --> pdb=" O LEU D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 268 removed outlier: 3.563A pdb=" N LEU D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 283 removed outlier: 3.663A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.854A pdb=" N THR D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 313 removed outlier: 3.572A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 338 through 360 removed outlier: 3.950A pdb=" N ASP D 342 " --> pdb=" O SER D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 403 through 407 Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 480 through 492 removed outlier: 3.516A pdb=" N TYR D 484 " --> pdb=" O ARG D 480 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 530 removed outlier: 3.573A pdb=" N CYS D 529 " --> pdb=" O HIS D 525 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR D 530 " --> pdb=" O PRO D 526 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 525 through 530' Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 580 through 589 Processing helix chain 'D' and resid 606 through 617 Processing helix chain 'D' and resid 636 through 640 removed outlier: 3.705A pdb=" N GLU D 640 " --> pdb=" O ARG D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 672 Processing helix chain 'D' and resid 685 through 699 Processing helix chain 'D' and resid 700 through 723 removed outlier: 3.877A pdb=" N GLY D 723 " --> pdb=" O ALA D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 757 removed outlier: 3.711A pdb=" N ARG D 757 " --> pdb=" O LYS D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 788 Processing helix chain 'D' and resid 792 through 800 Processing helix chain 'D' and resid 805 through 814 Processing helix chain 'D' and resid 840 through 876 removed outlier: 3.887A pdb=" N GLY D 850 " --> pdb=" O ILE D 846 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS D 853 " --> pdb=" O HIS D 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 910 through 915 removed outlier: 3.803A pdb=" N SER D 914 " --> pdb=" O ASP D 910 " (cutoff:3.500A) Processing helix chain 'D' and resid 939 through 950 Processing helix chain 'D' and resid 958 through 962 Processing helix chain 'D' and resid 969 through 974 removed outlier: 3.785A pdb=" N TYR D 973 " --> pdb=" O CYS D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 988 through 999 removed outlier: 3.556A pdb=" N ILE D 992 " --> pdb=" O ALA D 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 1000 through 1005 removed outlier: 4.634A pdb=" N THR D1005 " --> pdb=" O GLY D1001 " (cutoff:3.500A) Processing helix chain 'D' and resid 1022 through 1031 Processing helix chain 'D' and resid 1100 through 1108 Processing helix chain 'D' and resid 1109 through 1127 Processing helix chain 'D' and resid 1133 through 1145 removed outlier: 3.946A pdb=" N ILE D1137 " --> pdb=" O HIS D1133 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE D1140 " --> pdb=" O HIS D1136 " (cutoff:3.500A) Processing helix chain 'D' and resid 1166 through 1180 Processing helix chain 'D' and resid 1192 through 1199 Processing helix chain 'D' and resid 1202 through 1209 removed outlier: 3.569A pdb=" N SER D1208 " --> pdb=" O LEU D1204 " (cutoff:3.500A) Processing helix chain 'D' and resid 1211 through 1223 removed outlier: 3.798A pdb=" N VAL D1215 " --> pdb=" O GLU D1211 " (cutoff:3.500A) Processing helix chain 'D' and resid 1231 through 1237 Processing helix chain 'D' and resid 1247 through 1252 Processing helix chain 'D' and resid 1258 through 1265 Processing helix chain 'E' and resid 15 through 24 removed outlier: 4.161A pdb=" N LEU E 19 " --> pdb=" O PRO E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 45 removed outlier: 3.535A pdb=" N LEU E 29 " --> pdb=" O SER E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 78 Processing helix chain 'F' and resid 213 through 223 removed outlier: 3.976A pdb=" N ASP F 217 " --> pdb=" O ASP F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 252 Processing helix chain 'F' and resid 257 through 282 Processing helix chain 'F' and resid 282 through 292 Processing helix chain 'F' and resid 299 through 318 Processing helix chain 'F' and resid 325 through 346 removed outlier: 3.678A pdb=" N TYR F 329 " --> pdb=" O LYS F 325 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR F 331 " --> pdb=" O SER F 327 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TRP F 332 " --> pdb=" O THR F 328 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TRP F 333 " --> pdb=" O TYR F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 374 Processing helix chain 'F' and resid 378 through 387 removed outlier: 3.577A pdb=" N LEU F 386 " --> pdb=" O LEU F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 400 Processing helix chain 'F' and resid 417 through 421 removed outlier: 3.764A pdb=" N LEU F 421 " --> pdb=" O PHE F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 450 Processing helix chain 'F' and resid 451 through 463 Processing helix chain 'F' and resid 471 through 479 removed outlier: 3.669A pdb=" N LYS F 477 " --> pdb=" O ASP F 473 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N VAL F 478 " --> pdb=" O GLU F 474 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR F 479 " --> pdb=" O ILE F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 484 through 498 Processing helix chain 'F' and resid 500 through 502 No H-bonds generated for 'chain 'F' and resid 500 through 502' Processing helix chain 'F' and resid 503 through 508 removed outlier: 4.113A pdb=" N ASP F 508 " --> pdb=" O GLN F 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 26 removed outlier: 3.831A pdb=" N ALA G 17 " --> pdb=" O THR G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 43 Processing helix chain 'G' and resid 48 through 62 Processing helix chain 'G' and resid 101 through 116 removed outlier: 3.529A pdb=" N GLU G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 135 Processing helix chain 'H' and resid 13 through 26 Processing helix chain 'H' and resid 32 through 43 Processing helix chain 'H' and resid 47 through 62 Processing helix chain 'H' and resid 101 through 115 removed outlier: 3.764A pdb=" N GLU H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 135 removed outlier: 4.214A pdb=" N ALA H 134 " --> pdb=" O CYS H 130 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY H 135 " --> pdb=" O ALA H 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 130 through 135' Processing helix chain 'K' and resid 13 through 26 Processing helix chain 'K' and resid 31 through 42 Processing helix chain 'K' and resid 47 through 62 Processing helix chain 'K' and resid 101 through 115 removed outlier: 3.692A pdb=" N GLU K 105 " --> pdb=" O GLY K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 135 removed outlier: 4.096A pdb=" N ALA K 134 " --> pdb=" O CYS K 130 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY K 135 " --> pdb=" O ALA K 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 130 through 135' Processing helix chain 'L' and resid 13 through 25 Processing helix chain 'L' and resid 32 through 43 Processing helix chain 'L' and resid 48 through 62 Processing helix chain 'L' and resid 101 through 115 removed outlier: 3.828A pdb=" N GLU L 105 " --> pdb=" O GLY L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 135 removed outlier: 3.636A pdb=" N ALA L 134 " --> pdb=" O CYS L 130 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY L 135 " --> pdb=" O ALA L 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 130 through 135' Processing helix chain 'M' and resid 13 through 26 Processing helix chain 'M' and resid 31 through 43 Processing helix chain 'M' and resid 47 through 62 Processing helix chain 'M' and resid 101 through 116 removed outlier: 3.924A pdb=" N GLU M 105 " --> pdb=" O GLY M 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 135 Processing helix chain 'N' and resid 13 through 26 Processing helix chain 'N' and resid 31 through 43 Processing helix chain 'N' and resid 47 through 62 Processing helix chain 'N' and resid 101 through 116 removed outlier: 4.195A pdb=" N GLU N 105 " --> pdb=" O GLY N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 135 removed outlier: 4.162A pdb=" N ALA N 134 " --> pdb=" O CYS N 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 250 through 255 Processing helix chain 'S' and resid 257 through 267 Processing helix chain 'S' and resid 271 through 278 Processing helix chain 'S' and resid 279 through 286 removed outlier: 3.536A pdb=" N ILE S 286 " --> pdb=" O ASP S 282 " (cutoff:3.500A) Processing helix chain 'S' and resid 290 through 304 removed outlier: 3.751A pdb=" N MET S 304 " --> pdb=" O LYS S 300 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 15 removed outlier: 6.481A pdb=" N ARG A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.990A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.670A pdb=" N ALA A 126 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.693A pdb=" N LEU B 192 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N THR B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL B 183 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE B 189 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 98 removed outlier: 7.603A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 50 " --> pdb=" O GLU B 141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.532A pdb=" N GLY B 103 " --> pdb=" O LEU B 128 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 23 through 24 removed outlier: 6.339A pdb=" N ILE C 23 " --> pdb=" O ALA C 958 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 91 through 100 removed outlier: 5.486A pdb=" N LEU C 93 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N THR C 128 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N PHE C 95 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N GLU C 126 " --> pdb=" O PHE C 95 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ASP C 97 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA C 119 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ASP C 144 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LEU C 121 " --> pdb=" O MET C 142 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET C 142 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN C 129 " --> pdb=" O GLU C 134 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU C 134 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 154 through 156 Processing sheet with id=AB4, first strand: chain 'C' and resid 166 through 169 removed outlier: 3.502A pdb=" N GLN C 166 " --> pdb=" O ARG C 365 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 172 through 180 removed outlier: 3.667A pdb=" N ASP C 180 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS C 185 " --> pdb=" O ASP C 180 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE C 188 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 200 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 340 through 342 removed outlier: 3.510A pdb=" N THR C 341 " --> pdb=" O ILE C 349 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 440 through 442 removed outlier: 3.703A pdb=" N GLY C 484 " --> pdb=" O LEU C 441 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 491 through 492 removed outlier: 6.787A pdb=" N ILE C 498 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU C 517 " --> pdb=" O ILE C 498 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THR C 500 " --> pdb=" O ASP C 515 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASP C 515 " --> pdb=" O THR C 500 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TYR C 502 " --> pdb=" O ASP C 513 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASP C 513 " --> pdb=" O TYR C 502 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS C 504 " --> pdb=" O THR C 511 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 491 through 492 removed outlier: 3.859A pdb=" N ASP C 566 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 628 through 629 Processing sheet with id=AC2, first strand: chain 'C' and resid 634 through 639 removed outlier: 5.857A pdb=" N VAL C 636 " --> pdb=" O THR C 647 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N THR C 647 " --> pdb=" O VAL C 636 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU C 638 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 694 through 695 Processing sheet with id=AC4, first strand: chain 'C' and resid 992 through 993 removed outlier: 7.298A pdb=" N ILE C 721 " --> pdb=" O SER C 882 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE C 884 " --> pdb=" O ILE C 721 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU C 723 " --> pdb=" O ILE C 884 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N SER C1009 " --> pdb=" O PHE C 709 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 734 through 746 removed outlier: 3.686A pdb=" N HIS C 741 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY C 835 " --> pdb=" O TYR C 858 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ALA C 860 " --> pdb=" O VAL C 833 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N VAL C 833 " --> pdb=" O ALA C 860 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N LYS C 862 " --> pdb=" O GLY C 831 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N GLY C 831 " --> pdb=" O LYS C 862 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY C 831 " --> pdb=" O VAL C 782 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 754 through 755 Processing sheet with id=AC7, first strand: chain 'C' and resid 787 through 789 removed outlier: 3.887A pdb=" N VAL C 789 " --> pdb=" O LEU C 823 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 930 through 931 Processing sheet with id=AC9, first strand: chain 'C' and resid 1027 through 1029 removed outlier: 3.842A pdb=" N SER D 428 " --> pdb=" O MET D 541 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1052 through 1053 Processing sheet with id=AD2, first strand: chain 'C' and resid 1121 through 1123 removed outlier: 3.649A pdb=" N ASP D1226 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 93 through 96 removed outlier: 3.689A pdb=" N GLY D 93 " --> pdb=" O VAL D 319 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 135 through 139 removed outlier: 5.504A pdb=" N ILE D 136 " --> pdb=" O SER D 255 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N SER D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 336 through 337 Processing sheet with id=AD6, first strand: chain 'D' and resid 603 through 604 Processing sheet with id=AD7, first strand: chain 'D' and resid 820 through 821 Processing sheet with id=AD8, first strand: chain 'D' and resid 892 through 894 removed outlier: 3.907A pdb=" N MET D 919 " --> pdb=" O ARG D 957 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 1070 through 1073 removed outlier: 3.573A pdb=" N GLY D1046 " --> pdb=" O VAL D1088 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 1163 through 1165 Processing sheet with id=AE2, first strand: chain 'D' and resid 1253 through 1257 removed outlier: 3.505A pdb=" N ARG D1254 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU D1256 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR E 81 " --> pdb=" O GLU D1256 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 30 through 31 Processing sheet with id=AE4, first strand: chain 'G' and resid 96 through 99 removed outlier: 5.207A pdb=" N HIS G 87 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE G 126 " --> pdb=" O HIS G 87 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE G 127 " --> pdb=" O ALA H 121 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N HIS H 87 " --> pdb=" O VAL H 124 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ILE H 126 " --> pdb=" O HIS H 87 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL H 89 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY H 128 " --> pdb=" O VAL H 89 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 30 through 31 Processing sheet with id=AE6, first strand: chain 'K' and resid 64 through 68 Processing sheet with id=AE7, first strand: chain 'K' and resid 96 through 99 removed outlier: 4.955A pdb=" N HIS K 87 " --> pdb=" O VAL K 124 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE K 126 " --> pdb=" O HIS K 87 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE K 127 " --> pdb=" O ALA L 121 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N HIS L 87 " --> pdb=" O VAL L 124 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ILE L 126 " --> pdb=" O HIS L 87 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL L 89 " --> pdb=" O ILE L 126 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLY L 128 " --> pdb=" O VAL L 89 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 30 through 31 removed outlier: 3.832A pdb=" N ARG L 30 " --> pdb=" O TYR L 76 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 65 through 68 removed outlier: 3.611A pdb=" N ARG M 77 " --> pdb=" O ASP M 65 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 96 through 99 removed outlier: 5.133A pdb=" N HIS M 87 " --> pdb=" O VAL M 124 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE M 126 " --> pdb=" O HIS M 87 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR M 123 " --> pdb=" O GLU N 125 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU N 125 " --> pdb=" O THR M 123 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N HIS N 87 " --> pdb=" O VAL N 124 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 65 through 68 1492 hydrogen bonds defined for protein. 4263 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 165 hydrogen bonds 330 hydrogen bond angles 0 basepair planarities 62 basepair parallelities 125 stacking parallelities Total time for adding SS restraints: 17.82 Time building geometry restraints manager: 17.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11080 1.34 - 1.46: 6055 1.46 - 1.58: 18104 1.58 - 1.70: 334 1.70 - 1.82: 206 Bond restraints: 35779 Sorted by residual: bond pdb=" O3' DC O 28 " pdb=" P DC O 29 " ideal model delta sigma weight residual 1.607 1.652 -0.045 1.50e-02 4.44e+03 9.13e+00 bond pdb=" CA VAL C 908 " pdb=" CB VAL C 908 " ideal model delta sigma weight residual 1.534 1.554 -0.020 6.80e-03 2.16e+04 8.43e+00 bond pdb=" O3' DG O 25 " pdb=" P DT O 26 " ideal model delta sigma weight residual 1.607 1.645 -0.038 1.50e-02 4.44e+03 6.47e+00 bond pdb=" CA VAL C 908 " pdb=" C VAL C 908 " ideal model delta sigma weight residual 1.520 1.541 -0.021 8.80e-03 1.29e+04 5.89e+00 bond pdb=" CA GLY C1049 " pdb=" C GLY C1049 " ideal model delta sigma weight residual 1.520 1.503 0.017 7.30e-03 1.88e+04 5.53e+00 ... (remaining 35774 not shown) Histogram of bond angle deviations from ideal: 98.39 - 105.56: 1316 105.56 - 112.72: 19016 112.72 - 119.89: 12637 119.89 - 127.05: 15463 127.05 - 134.22: 687 Bond angle restraints: 49119 Sorted by residual: angle pdb=" O3' DC O 23 " pdb=" C3' DC O 23 " pdb=" C2' DC O 23 " ideal model delta sigma weight residual 111.50 99.00 12.50 1.50e+00 4.44e-01 6.94e+01 angle pdb=" N ARG C1029 " pdb=" CA ARG C1029 " pdb=" C ARG C1029 " ideal model delta sigma weight residual 107.20 118.65 -11.45 1.70e+00 3.46e-01 4.53e+01 angle pdb=" N LYS D 64 " pdb=" CA LYS D 64 " pdb=" C LYS D 64 " ideal model delta sigma weight residual 111.07 117.38 -6.31 1.07e+00 8.73e-01 3.48e+01 angle pdb=" O3' DG P 62 " pdb=" C3' DG P 62 " pdb=" C2' DG P 62 " ideal model delta sigma weight residual 111.50 103.02 8.48 1.50e+00 4.44e-01 3.20e+01 angle pdb=" N THR D1213 " pdb=" CA THR D1213 " pdb=" C THR D1213 " ideal model delta sigma weight residual 111.07 116.98 -5.91 1.07e+00 8.73e-01 3.05e+01 ... (remaining 49114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 20028 35.66 - 71.32: 1123 71.32 - 106.98: 49 106.98 - 142.65: 3 142.65 - 178.31: 14 Dihedral angle restraints: 21217 sinusoidal: 9616 harmonic: 11601 Sorted by residual: dihedral pdb=" C VAL C 908 " pdb=" N VAL C 908 " pdb=" CA VAL C 908 " pdb=" CB VAL C 908 " ideal model delta harmonic sigma weight residual -122.00 -133.45 11.45 0 2.50e+00 1.60e-01 2.10e+01 dihedral pdb=" C4' DT P 76 " pdb=" C3' DT P 76 " pdb=" O3' DT P 76 " pdb=" P DG P 77 " ideal model delta sinusoidal sigma weight residual -140.00 38.31 -178.31 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT P 73 " pdb=" C3' DT P 73 " pdb=" O3' DT P 73 " pdb=" P DC P 74 " ideal model delta sinusoidal sigma weight residual 220.00 46.97 173.03 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 21214 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 4902 0.069 - 0.138: 622 0.138 - 0.207: 39 0.207 - 0.275: 11 0.275 - 0.344: 7 Chirality restraints: 5581 Sorted by residual: chirality pdb=" CA VAL C 908 " pdb=" N VAL C 908 " pdb=" C VAL C 908 " pdb=" CB VAL C 908 " both_signs ideal model delta sigma weight residual False 2.44 2.10 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" C3' DG O 20 " pdb=" C4' DG O 20 " pdb=" O3' DG O 20 " pdb=" C2' DG O 20 " both_signs ideal model delta sigma weight residual False -2.66 -2.32 -0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CA THR H 54 " pdb=" N THR H 54 " pdb=" C THR H 54 " pdb=" CB THR H 54 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.32 2.00e-01 2.50e+01 2.61e+00 ... (remaining 5578 not shown) Planarity restraints: 5854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP C 215 " -0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" CG ASP C 215 " 0.058 2.00e-02 2.50e+03 pdb=" OD1 ASP C 215 " -0.021 2.00e-02 2.50e+03 pdb=" OD2 ASP C 215 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 593 " -0.014 2.00e-02 2.50e+03 2.70e-02 7.28e+00 pdb=" C GLU D 593 " 0.047 2.00e-02 2.50e+03 pdb=" O GLU D 593 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY D 594 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 474 " -0.044 5.00e-02 4.00e+02 6.67e-02 7.12e+00 pdb=" N PRO C 475 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 475 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 475 " -0.037 5.00e-02 4.00e+02 ... (remaining 5851 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 257 2.55 - 3.14: 28413 3.14 - 3.73: 57983 3.73 - 4.31: 75165 4.31 - 4.90: 122773 Nonbonded interactions: 284591 Sorted by model distance: nonbonded pdb=" OD2 ASP L 65 " pdb="ZN ZN L 202 " model vdw 1.963 2.230 nonbonded pdb=" OD2 ASP N 65 " pdb="ZN ZN N 202 " model vdw 1.969 2.230 nonbonded pdb=" OE2 GLU N 105 " pdb="ZN ZN N 203 " model vdw 1.997 2.230 nonbonded pdb=" OD2 ASP K 65 " pdb="ZN ZN K 202 " model vdw 2.015 2.230 nonbonded pdb=" OD2 ASP D 539 " pdb="MG MG D1401 " model vdw 2.020 2.170 ... (remaining 284586 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 2 through 227) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 13.300 Check model and map are aligned: 0.520 Set scattering table: 0.300 Process input model: 110.020 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 35779 Z= 0.266 Angle : 0.752 12.498 49119 Z= 0.421 Chirality : 0.047 0.344 5581 Planarity : 0.004 0.086 5854 Dihedral : 19.815 178.307 13749 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.66 % Allowed : 19.99 % Favored : 79.36 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.13), residues: 4029 helix: 1.31 (0.13), residues: 1656 sheet: -0.44 (0.24), residues: 459 loop : -0.39 (0.14), residues: 1914 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 362 time to evaluate : 3.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 9 residues processed: 381 average time/residue: 0.5249 time to fit residues: 324.0252 Evaluate side-chains 289 residues out of total 3353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 280 time to evaluate : 3.775 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3266 time to fit residues: 10.5938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 352 optimal weight: 8.9990 chunk 316 optimal weight: 2.9990 chunk 175 optimal weight: 40.0000 chunk 107 optimal weight: 3.9990 chunk 213 optimal weight: 0.2980 chunk 168 optimal weight: 2.9990 chunk 326 optimal weight: 50.0000 chunk 126 optimal weight: 0.8980 chunk 198 optimal weight: 0.9980 chunk 243 optimal weight: 0.9990 chunk 378 optimal weight: 50.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 152 ASN C 374 GLN C 424 GLN C 429 ASN C 916 GLN C 980 ASN C1040 GLN D 213 GLN D 416 ASN D 440 GLN D 669 ASN ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 35779 Z= 0.291 Angle : 0.640 8.627 49119 Z= 0.341 Chirality : 0.044 0.293 5581 Planarity : 0.004 0.065 5854 Dihedral : 19.984 179.926 6103 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.13 % Allowed : 18.50 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.13), residues: 4029 helix: 1.29 (0.12), residues: 1681 sheet: -0.32 (0.23), residues: 469 loop : -0.53 (0.14), residues: 1879 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 318 time to evaluate : 3.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 44 residues processed: 402 average time/residue: 0.4602 time to fit residues: 308.3846 Evaluate side-chains 317 residues out of total 3353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 273 time to evaluate : 3.593 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.3633 time to fit residues: 33.8698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 210 optimal weight: 0.6980 chunk 117 optimal weight: 0.8980 chunk 315 optimal weight: 8.9990 chunk 257 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 379 optimal weight: 40.0000 chunk 409 optimal weight: 10.0000 chunk 337 optimal weight: 50.0000 chunk 376 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 chunk 304 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN C 465 HIS C 941 GLN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 GLN D 384 ASN D 579 GLN D1021 GLN D1102 HIS ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 371 GLN ** H 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 35779 Z= 0.355 Angle : 0.656 12.477 49119 Z= 0.346 Chirality : 0.044 0.209 5581 Planarity : 0.005 0.062 5854 Dihedral : 19.996 177.007 6103 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.28 % Allowed : 19.99 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.13), residues: 4029 helix: 1.22 (0.13), residues: 1667 sheet: -0.40 (0.23), residues: 486 loop : -0.63 (0.14), residues: 1876 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 319 time to evaluate : 3.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 110 outliers final: 50 residues processed: 407 average time/residue: 0.4490 time to fit residues: 301.9673 Evaluate side-chains 330 residues out of total 3353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 280 time to evaluate : 3.387 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.3325 time to fit residues: 36.3952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 374 optimal weight: 40.0000 chunk 285 optimal weight: 0.5980 chunk 196 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 181 optimal weight: 0.7980 chunk 254 optimal weight: 0.5980 chunk 380 optimal weight: 30.0000 chunk 403 optimal weight: 7.9990 chunk 198 optimal weight: 0.5980 chunk 360 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 HIS C 885 ASN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 GLN F 252 ASN K 36 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35779 Z= 0.205 Angle : 0.588 13.026 49119 Z= 0.312 Chirality : 0.042 0.308 5581 Planarity : 0.004 0.060 5854 Dihedral : 19.928 176.961 6103 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.27 % Allowed : 21.39 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.13), residues: 4029 helix: 1.45 (0.13), residues: 1681 sheet: -0.20 (0.23), residues: 490 loop : -0.54 (0.14), residues: 1858 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 322 time to evaluate : 3.881 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 outliers start: 76 outliers final: 39 residues processed: 383 average time/residue: 0.4790 time to fit residues: 304.5642 Evaluate side-chains 320 residues out of total 3353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 281 time to evaluate : 3.652 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.3541 time to fit residues: 30.2035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 335 optimal weight: 40.0000 chunk 228 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 300 optimal weight: 0.6980 chunk 166 optimal weight: 0.4980 chunk 343 optimal weight: 7.9990 chunk 278 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 205 optimal weight: 2.9990 chunk 361 optimal weight: 20.0000 chunk 101 optimal weight: 0.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN C 465 HIS ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 GLN D 384 ASN D 579 GLN D 877 GLN ** D1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 35779 Z= 0.312 Angle : 0.628 11.533 49119 Z= 0.331 Chirality : 0.043 0.403 5581 Planarity : 0.004 0.059 5854 Dihedral : 19.932 177.651 6103 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.45 % Allowed : 22.23 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.13), residues: 4029 helix: 1.36 (0.13), residues: 1672 sheet: -0.23 (0.23), residues: 482 loop : -0.65 (0.14), residues: 1875 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 292 time to evaluate : 3.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 43 residues processed: 354 average time/residue: 0.4987 time to fit residues: 290.3278 Evaluate side-chains 316 residues out of total 3353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 273 time to evaluate : 3.650 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.3357 time to fit residues: 32.0122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 135 optimal weight: 0.9980 chunk 362 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 236 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 403 optimal weight: 7.9990 chunk 334 optimal weight: 50.0000 chunk 186 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 211 optimal weight: 0.5980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 424 GLN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 579 GLN ** D1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 488 GLN N 36 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 35779 Z= 0.314 Angle : 0.631 10.061 49119 Z= 0.332 Chirality : 0.043 0.338 5581 Planarity : 0.004 0.058 5854 Dihedral : 19.927 178.063 6103 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.91 % Allowed : 23.12 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.13), residues: 4029 helix: 1.34 (0.13), residues: 1670 sheet: -0.30 (0.23), residues: 481 loop : -0.68 (0.14), residues: 1878 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 291 time to evaluate : 3.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 28 residues processed: 339 average time/residue: 0.4938 time to fit residues: 278.2169 Evaluate side-chains 297 residues out of total 3353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 269 time to evaluate : 3.877 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3354 time to fit residues: 22.9949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 388 optimal weight: 0.0970 chunk 45 optimal weight: 0.7980 chunk 229 optimal weight: 1.9990 chunk 294 optimal weight: 9.9990 chunk 228 optimal weight: 2.9990 chunk 339 optimal weight: 40.0000 chunk 225 optimal weight: 2.9990 chunk 401 optimal weight: 4.9990 chunk 251 optimal weight: 3.9990 chunk 245 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 ASN D 384 ASN D 579 GLN ** D1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN F 371 GLN F 488 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 35779 Z= 0.363 Angle : 0.669 9.792 49119 Z= 0.349 Chirality : 0.044 0.307 5581 Planarity : 0.005 0.059 5854 Dihedral : 19.950 178.479 6103 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.64 % Allowed : 24.28 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.13), residues: 4029 helix: 1.23 (0.13), residues: 1675 sheet: -0.30 (0.23), residues: 480 loop : -0.80 (0.14), residues: 1874 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 287 time to evaluate : 3.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 23 residues processed: 327 average time/residue: 0.4716 time to fit residues: 255.6283 Evaluate side-chains 289 residues out of total 3353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 266 time to evaluate : 3.655 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.4020 time to fit residues: 23.1972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 248 optimal weight: 7.9990 chunk 160 optimal weight: 0.8980 chunk 240 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 255 optimal weight: 1.9990 chunk 273 optimal weight: 0.4980 chunk 198 optimal weight: 0.6980 chunk 37 optimal weight: 20.0000 chunk 315 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1116 HIS F 305 GLN F 371 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 35779 Z= 0.224 Angle : 0.624 14.660 49119 Z= 0.326 Chirality : 0.042 0.274 5581 Planarity : 0.004 0.054 5854 Dihedral : 19.881 179.545 6103 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.10 % Allowed : 24.82 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.13), residues: 4029 helix: 1.49 (0.13), residues: 1663 sheet: -0.24 (0.23), residues: 480 loop : -0.71 (0.14), residues: 1886 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 301 time to evaluate : 3.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 17 residues processed: 332 average time/residue: 0.4768 time to fit residues: 261.7386 Evaluate side-chains 290 residues out of total 3353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 273 time to evaluate : 3.394 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.3217 time to fit residues: 15.2045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 365 optimal weight: 50.0000 chunk 385 optimal weight: 10.0000 chunk 351 optimal weight: 40.0000 chunk 374 optimal weight: 50.0000 chunk 384 optimal weight: 9.9990 chunk 225 optimal weight: 0.7980 chunk 163 optimal weight: 0.1980 chunk 294 optimal weight: 9.9990 chunk 114 optimal weight: 0.2980 chunk 338 optimal weight: 50.0000 chunk 354 optimal weight: 50.0000 overall best weight: 4.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 GLN C 916 GLN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 ASN ** D 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 GLN D1116 HIS ** F 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 488 GLN G 15 GLN H 15 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.102 35779 Z= 0.765 Angle : 0.886 13.653 49119 Z= 0.461 Chirality : 0.053 0.386 5581 Planarity : 0.006 0.082 5854 Dihedral : 20.116 179.756 6103 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.34 % Allowed : 25.27 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.13), residues: 4029 helix: 0.65 (0.12), residues: 1691 sheet: -0.57 (0.23), residues: 472 loop : -1.16 (0.14), residues: 1866 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 265 time to evaluate : 3.731 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 outliers start: 45 outliers final: 18 residues processed: 296 average time/residue: 0.4809 time to fit residues: 236.0352 Evaluate side-chains 271 residues out of total 3353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 253 time to evaluate : 3.677 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3290 time to fit residues: 16.2016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 373 optimal weight: 6.9990 chunk 245 optimal weight: 0.9990 chunk 396 optimal weight: 70.0000 chunk 241 optimal weight: 1.9990 chunk 187 optimal weight: 0.7980 chunk 275 optimal weight: 0.9990 chunk 415 optimal weight: 30.0000 chunk 382 optimal weight: 9.9990 chunk 330 optimal weight: 50.0000 chunk 34 optimal weight: 10.0000 chunk 255 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1116 HIS ** F 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 488 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 35779 Z= 0.279 Angle : 0.672 14.216 49119 Z= 0.349 Chirality : 0.044 0.316 5581 Planarity : 0.005 0.060 5854 Dihedral : 19.990 179.471 6103 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.24 % Allowed : 25.84 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.13), residues: 4029 helix: 1.14 (0.13), residues: 1678 sheet: -0.41 (0.23), residues: 490 loop : -1.01 (0.14), residues: 1861 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 293 time to evaluate : 3.657 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 outliers start: 8 outliers final: 4 residues processed: 299 average time/residue: 0.5021 time to fit residues: 248.1208 Evaluate side-chains 275 residues out of total 3353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 271 time to evaluate : 3.674 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4669 time to fit residues: 8.2329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 202 optimal weight: 4.9990 chunk 262 optimal weight: 0.9980 chunk 352 optimal weight: 40.0000 chunk 101 optimal weight: 1.9990 chunk 305 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 331 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 340 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 ASN ** D 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.186497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.132823 restraints weight = 56702.308| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 3.65 r_work: 0.3317 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 35779 Z= 0.285 Angle : 0.677 14.832 49119 Z= 0.351 Chirality : 0.043 0.304 5581 Planarity : 0.004 0.057 5854 Dihedral : 19.956 179.822 6103 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.45 % Allowed : 26.31 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.13), residues: 4029 helix: 1.23 (0.13), residues: 1677 sheet: -0.33 (0.23), residues: 492 loop : -0.95 (0.14), residues: 1860 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7581.24 seconds wall clock time: 139 minutes 2.49 seconds (8342.49 seconds total)