Starting phenix.real_space_refine on Fri Feb 23 15:12:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffz_29071/02_2024/8ffz_29071.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffz_29071/02_2024/8ffz_29071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffz_29071/02_2024/8ffz_29071.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffz_29071/02_2024/8ffz_29071.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffz_29071/02_2024/8ffz_29071.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffz_29071/02_2024/8ffz_29071.pdb" } resolution = 3.8 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= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians Zn 9 6.06 5 P 302 5.49 5 S 143 5.16 5 C 23882 2.51 5 N 6695 2.21 5 O 7931 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 62": "NH1" <-> "NH2" Residue "A ARG 78": "NH1" <-> "NH2" Residue "A ARG 97": "NH1" <-> "NH2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A ARG 125": "NH1" <-> "NH2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 179": "NH1" <-> "NH2" Residue "A ARG 206": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 366": "NH1" <-> "NH2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B ARG 144": "NH1" <-> "NH2" Residue "B ARG 186": "NH1" <-> "NH2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B ARG 204": "NH1" <-> "NH2" Residue "B ARG 211": "NH1" <-> "NH2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B ARG 330": "NH1" <-> "NH2" Residue "B ARG 358": "NH1" <-> "NH2" Residue "B ARG 366": "NH1" <-> "NH2" Residue "B ARG 390": "NH1" <-> "NH2" Residue "B ARG 393": "NH1" <-> "NH2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B ARG 435": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 548": "NH1" <-> "NH2" Residue "B ARG 551": "NH1" <-> "NH2" Residue "B ARG 555": "NH1" <-> "NH2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B ARG 573": "NH1" <-> "NH2" Residue "B ARG 596": "NH1" <-> "NH2" Residue "B ARG 611": "NH1" <-> "NH2" Residue "B ARG 618": "NH1" <-> "NH2" Residue "B PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 633": "NH1" <-> "NH2" Residue "B ARG 748": "NH1" <-> "NH2" Residue "B ARG 784": "NH1" <-> "NH2" Residue "B ARG 785": "NH1" <-> "NH2" Residue "B ARG 787": "NH1" <-> "NH2" Residue "B ARG 794": "NH1" <-> "NH2" Residue "B ARG 816": "NH1" <-> "NH2" Residue "B ARG 840": "NH1" <-> "NH2" Residue "B ARG 852": "NH1" <-> "NH2" Residue "B ARG 859": "NH1" <-> "NH2" Residue "B ARG 878": "NH1" <-> "NH2" Residue "B ARG 889": "NH1" <-> "NH2" Residue "B ARG 908": "NH1" <-> "NH2" Residue "B ARG 912": "NH1" <-> "NH2" Residue "B ARG 970": "NH1" <-> "NH2" Residue "B TYR 973": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 983": "NH1" <-> "NH2" Residue "B ARG 1043": "NH1" <-> "NH2" Residue "B ARG 1063": "NH1" <-> "NH2" Residue "B ARG 1077": "NH1" <-> "NH2" Residue "B ARG 1087": "NH1" <-> "NH2" Residue "B ARG 1112": "NH1" <-> "NH2" Residue "B ARG 1116": "NH1" <-> "NH2" Residue "B ARG 1118": "NH1" <-> "NH2" Residue "B ARG 1136": "NH1" <-> "NH2" Residue "C ARG 141": "NH1" <-> "NH2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C ARG 160": "NH1" <-> "NH2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "C ARG 235": "NH1" <-> "NH2" Residue "C ARG 236": "NH1" <-> "NH2" Residue "C ARG 248": "NH1" <-> "NH2" Residue "C ARG 255": "NH1" <-> "NH2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C ARG 279": "NH1" <-> "NH2" Residue "C ARG 297": "NH1" <-> "NH2" Residue "C ARG 298": "NH1" <-> "NH2" Residue "C ARG 335": "NH1" <-> "NH2" Residue "C ARG 386": "NH1" <-> "NH2" Residue "C ARG 390": "NH1" <-> "NH2" Residue "C ARG 391": "NH1" <-> "NH2" Residue "C PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 409": "NH1" <-> "NH2" Residue "C ARG 410": "NH1" <-> "NH2" Residue "C ARG 435": "NH1" <-> "NH2" Residue "C ARG 437": "NH1" <-> "NH2" Residue "C ARG 442": "NH1" <-> "NH2" Residue "C ARG 479": "NH1" <-> "NH2" Residue "C ARG 500": "NH1" <-> "NH2" Residue "C ARG 510": "NH1" <-> "NH2" Residue "C ARG 539": "NH1" <-> "NH2" Residue "C ARG 548": "NH1" <-> "NH2" Residue "C ARG 566": "NH1" <-> "NH2" Residue "C ARG 576": "NH1" <-> "NH2" Residue "C ARG 615": "NH1" <-> "NH2" Residue "C ARG 617": "NH1" <-> "NH2" Residue "C ARG 620": "NH1" <-> "NH2" Residue "C ARG 622": "NH1" <-> "NH2" Residue "C ARG 623": "NH1" <-> "NH2" Residue "C ARG 718": "NH1" <-> "NH2" Residue "C ARG 728": "NH1" <-> "NH2" Residue "C ARG 774": "NH1" <-> "NH2" Residue "C ARG 800": "NH1" <-> "NH2" Residue "C ARG 810": "NH1" <-> "NH2" Residue "C ARG 822": "NH1" <-> "NH2" Residue "C ARG 841": "NH1" <-> "NH2" Residue "C ARG 850": "NH1" <-> "NH2" Residue "C ARG 889": "NH1" <-> "NH2" Residue "C ARG 900": "NH1" <-> "NH2" Residue "C ARG 922": "NH1" <-> "NH2" Residue "C ARG 926": "NH1" <-> "NH2" Residue "C ARG 931": "NH1" <-> "NH2" Residue "C ARG 940": "NH1" <-> "NH2" Residue "C ARG 944": "NH1" <-> "NH2" Residue "C ARG 949": "NH1" <-> "NH2" Residue "C ARG 967": "NH1" <-> "NH2" Residue "C ARG 984": "NH1" <-> "NH2" Residue "D PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 35": "NH1" <-> "NH2" Residue "D ARG 107": "NH1" <-> "NH2" Residue "D ARG 111": "NH1" <-> "NH2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D ARG 161": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 216": "NH1" <-> "NH2" Residue "E ARG 155": "NH1" <-> "NH2" Residue "E ARG 158": "NH1" <-> "NH2" Residue "E ARG 167": "NH1" <-> "NH2" Residue "E ARG 172": "NH1" <-> "NH2" Residue "E ARG 232": "NH1" <-> "NH2" Residue "E ARG 250": "NH1" <-> "NH2" Residue "E ARG 253": "NH1" <-> "NH2" Residue "E ARG 281": "NH1" <-> "NH2" Residue "E ARG 282": "NH1" <-> "NH2" Residue "E PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 508": "NH1" <-> "NH2" Residue "E ARG 510": "NH1" <-> "NH2" Residue "E ARG 536": "NH1" <-> "NH2" Residue "E ARG 541": "NH1" <-> "NH2" Residue "E ARG 552": "NH1" <-> "NH2" Residue "E ARG 563": "NH1" <-> "NH2" Residue "E ARG 584": "NH1" <-> "NH2" Residue "E ARG 585": "NH1" <-> "NH2" Residue "E ARG 601": "NH1" <-> "NH2" Residue "E ARG 615": "NH1" <-> "NH2" Residue "E TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 11": "NH1" <-> "NH2" Residue "F ARG 25": "NH1" <-> "NH2" Residue "F ARG 89": "NH1" <-> "NH2" Residue "F ARG 130": "NH1" <-> "NH2" Residue "F ARG 159": "NH1" <-> "NH2" Residue "F ARG 175": "NH1" <-> "NH2" Residue "F ARG 219": "NH1" <-> "NH2" Residue "F ARG 226": "NH1" <-> "NH2" Residue "F ARG 227": "NH1" <-> "NH2" Residue "F ARG 353": "NH1" <-> "NH2" Residue "F ARG 382": "NH1" <-> "NH2" Residue "F ARG 437": "NH1" <-> "NH2" Residue "F ARG 487": "NH1" <-> "NH2" Residue "F ARG 529": "NH1" <-> "NH2" Residue "F ARG 551": "NH1" <-> "NH2" Residue "F ARG 557": "NH1" <-> "NH2" Residue "F ARG 568": "NH1" <-> "NH2" Residue "F ARG 573": "NH1" <-> "NH2" Residue "G TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 10": "NH1" <-> "NH2" Residue "G ARG 14": "NH1" <-> "NH2" Residue "G ARG 68": "NH1" <-> "NH2" Residue "G ARG 88": "NH1" <-> "NH2" Residue "G ARG 95": "NH1" <-> "NH2" Residue "G ARG 98": "NH1" <-> "NH2" Residue "G ARG 142": "NH1" <-> "NH2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G ARG 187": "NH1" <-> "NH2" Residue "G ARG 198": "NH1" <-> "NH2" Residue "G ARG 234": "NH1" <-> "NH2" Residue "G ARG 308": "NH1" <-> "NH2" Residue "G ARG 330": "NH1" <-> "NH2" Residue "G ARG 334": "NH1" <-> "NH2" Residue "G ARG 342": "NH1" <-> "NH2" Residue "G ARG 422": "NH1" <-> "NH2" Residue "G ARG 426": "NH1" <-> "NH2" Residue "G ARG 433": "NH1" <-> "NH2" Residue "H ARG 208": "NH1" <-> "NH2" Residue "H ARG 218": "NH1" <-> "NH2" Residue "H ARG 219": "NH1" <-> "NH2" Residue "H ARG 233": "NH1" <-> "NH2" Residue "H ARG 238": "NH1" <-> "NH2" Residue "H ARG 239": "NH1" <-> "NH2" Residue "H ARG 258": "NH1" <-> "NH2" Residue "H ARG 276": "NH1" <-> "NH2" Residue "H ARG 286": "NH1" <-> "NH2" Residue "H ARG 294": "NH1" <-> "NH2" Residue "H ARG 405": "NH1" <-> "NH2" Residue "H ARG 416": "NH1" <-> "NH2" Residue "H ARG 424": "NH1" <-> "NH2" Residue "H ARG 431": "NH1" <-> "NH2" Residue "H ARG 433": "NH1" <-> "NH2" Residue "H ARG 463": "NH1" <-> "NH2" Residue "H ARG 467": "NH1" <-> "NH2" Residue "H ARG 497": "NH1" <-> "NH2" Residue "H ARG 522": "NH1" <-> "NH2" Residue "H ARG 546": "NH1" <-> "NH2" Residue "H ARG 564": "NH1" <-> "NH2" Residue "H ARG 580": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 38962 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2597 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 14, 'TRANS': 299} Chain breaks: 1 Chain: "B" Number of atoms: 7330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7330 Classifications: {'peptide': 905} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 884} Chain breaks: 10 Chain: "C" Number of atoms: 6627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 6627 Classifications: {'peptide': 797} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 780} Chain breaks: 4 Chain: "D" Number of atoms: 2070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2070 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 19, 'TRANS': 242} Chain breaks: 1 Chain: "E" Number of atoms: 4097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 4097 Classifications: {'peptide': 518} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 497} Chain: "F" Number of atoms: 4743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4743 Classifications: {'peptide': 585} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 561} Chain breaks: 1 Chain: "G" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2705 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 312} Chain breaks: 3 Chain: "H" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2593 Classifications: {'peptide': 328} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 312} Chain breaks: 2 Chain: "I" Number of atoms: 3090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3090 Classifications: {'DNA': 151} Link IDs: {'rna3p': 150} Chain: "J" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3101 Classifications: {'DNA': 151} Link IDs: {'rna3p': 150} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Unusual residues: {' ZN': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 71 SG CYS A 51 87.429 188.358 105.624 1.00 27.87 S ATOM 109 SG CYS A 56 86.797 189.564 108.803 1.00 20.37 S ATOM 318 SG CYS A 82 96.600 214.796 101.474 1.00 49.44 S ATOM 341 SG CYS A 85 97.617 214.810 104.633 1.00 55.29 S ATOM 551 SG CYS A 110 76.109 228.679 109.884 1.00 62.54 S ATOM 575 SG CYS A 113 78.360 230.494 111.423 1.00 64.46 S ATOM 760 SG CYS A 136 63.455 223.527 133.606 1.00 80.62 S ATOM 795 SG CYS A 141 60.787 225.486 134.552 1.00 76.77 S ATOM 1001 SG CYS A 165 68.705 227.460 157.221 1.00 70.54 S ATOM 1024 SG CYS A 168 67.926 230.622 157.662 1.00 67.53 S ATOM 1501 SG CYS A 224 106.714 218.181 141.932 1.00 49.13 S ATOM 1522 SG CYS A 227 105.478 217.112 139.122 1.00 45.50 S ATOM 1741 SG CYS A 255 116.037 215.475 122.996 1.00 72.42 S ATOM 1765 SG CYS A 258 116.810 215.505 119.704 1.00 88.46 S ATOM 2339 SG CYS A 367 78.271 220.702 204.798 1.00144.51 S ATOM 2384 SG CYS A 372 81.244 222.045 205.959 1.00139.56 S ATOM 1270 SG CYS A 196 90.724 219.503 158.311 1.00 42.23 S ATOM 1303 SG CYS A 201 92.749 217.017 159.443 1.00 42.83 S Time building chain proxies: 20.62, per 1000 atoms: 0.53 Number of scatterers: 38962 At special positions: 0 Unit cell: (146.784, 267.168, 228.096, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 9 29.99 S 143 16.00 P 302 15.00 O 7931 8.00 N 6695 7.00 C 23882 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: 17.37 Conformation dependent library (CDL) restraints added in 5.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 74 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 69 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 56 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 51 " pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 85 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 82 " pdb="ZN ZN A 502 " - pdb=" NE2 HIS A 98 " pdb="ZN ZN A 502 " - pdb=" NE2 HIS A 102 " pdb=" ZN A 503 " pdb="ZN ZN A 503 " - pdb=" NE2 HIS A 126 " pdb="ZN ZN A 503 " - pdb=" SG CYS A 110 " pdb="ZN ZN A 503 " - pdb=" SG CYS A 113 " pdb=" ZN A 504 " pdb="ZN ZN A 504 " - pdb=" SG CYS A 141 " pdb="ZN ZN A 504 " - pdb=" NE2 HIS A 159 " pdb="ZN ZN A 504 " - pdb=" SG CYS A 136 " pdb="ZN ZN A 504 " - pdb=" NE2 HIS A 154 " pdb=" ZN A 505 " pdb="ZN ZN A 505 " - pdb=" SG CYS A 168 " pdb="ZN ZN A 505 " - pdb=" SG CYS A 165 " pdb="ZN ZN A 505 " - pdb=" NE2 HIS A 181 " pdb="ZN ZN A 505 " - pdb=" NE2 HIS A 186 " pdb=" ZN A 506 " pdb="ZN ZN A 506 " - pdb=" NE2 HIS A 244 " pdb="ZN ZN A 506 " - pdb=" SG CYS A 227 " pdb="ZN ZN A 506 " - pdb=" SG CYS A 224 " pdb="ZN ZN A 506 " - pdb=" NE2 HIS A 240 " pdb=" ZN A 507 " pdb="ZN ZN A 507 " - pdb=" NE2 HIS A 272 " pdb="ZN ZN A 507 " - pdb=" SG CYS A 255 " pdb="ZN ZN A 507 " - pdb=" SG CYS A 258 " pdb=" ZN A 508 " pdb="ZN ZN A 508 " - pdb=" SG CYS A 367 " pdb="ZN ZN A 508 " - pdb=" SG CYS A 372 " pdb="ZN ZN A 508 " - pdb=" NE2 HIS A 389 " pdb="ZN ZN A 508 " - pdb=" NE2 HIS A 385 " pdb=" ZN A 509 " pdb="ZN ZN A 509 " - pdb=" NE2 HIS A 219 " pdb="ZN ZN A 509 " - pdb=" SG CYS A 201 " pdb="ZN ZN A 509 " - pdb=" SG CYS A 196 " pdb="ZN ZN A 509 " - pdb=" NE2 HIS A 214 " Number of angles added : 14 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7754 Finding SS restraints... Secondary structure from input PDB file: 155 helices and 41 sheets defined 46.0% alpha, 15.5% beta 111 base pairs and 240 stacking pairs defined. Time for finding SS restraints: 13.85 Creating SS restraints... Processing helix chain 'A' and resid 62 through 74 removed outlier: 3.569A pdb=" N LEU A 66 " --> pdb=" O ARG A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.538A pdb=" N TYR A 100 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR A 101 " --> pdb=" O ARG A 97 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N HIS A 102 " --> pdb=" O HIS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 130 removed outlier: 3.768A pdb=" N HIS A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 159 removed outlier: 3.812A pdb=" N LEU A 151 " --> pdb=" O LYS A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.729A pdb=" N HIS A 186 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 219 removed outlier: 3.550A pdb=" N LEU A 211 " --> pdb=" O ILE A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.737A pdb=" N ILE A 242 " --> pdb=" O GLN A 238 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE A 243 " --> pdb=" O MET A 239 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N HIS A 244 " --> pdb=" O HIS A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 274 removed outlier: 3.889A pdb=" N THR A 271 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N HIS A 272 " --> pdb=" O ASP A 268 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 Processing helix chain 'A' and resid 332 through 349 Processing helix chain 'A' and resid 353 through 362 Processing helix chain 'A' and resid 378 through 396 Processing helix chain 'B' and resid 8 through 21 removed outlier: 4.024A pdb=" N GLN B 12 " --> pdb=" O ASP B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 36 removed outlier: 3.833A pdb=" N LYS B 36 " --> pdb=" O ASP B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 56 removed outlier: 3.826A pdb=" N LYS B 56 " --> pdb=" O CYS B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 78 Processing helix chain 'B' and resid 88 through 98 Processing helix chain 'B' and resid 107 through 121 Processing helix chain 'B' and resid 127 through 135 Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.613A pdb=" N LYS B 146 " --> pdb=" O THR B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 184 through 199 removed outlier: 4.169A pdb=" N HIS B 188 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ALA B 190 " --> pdb=" O ARG B 186 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N THR B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 213 Processing helix chain 'B' and resid 218 through 235 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 333 through 345 Processing helix chain 'B' and resid 346 through 349 Processing helix chain 'B' and resid 352 through 360 Processing helix chain 'B' and resid 361 through 363 No H-bonds generated for 'chain 'B' and resid 361 through 363' Processing helix chain 'B' and resid 364 through 373 Processing helix chain 'B' and resid 408 through 417 removed outlier: 4.270A pdb=" N PHE B 412 " --> pdb=" O THR B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 445 Processing helix chain 'B' and resid 549 through 565 removed outlier: 3.568A pdb=" N LEU B 560 " --> pdb=" O GLN B 556 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS B 561 " --> pdb=" O ARG B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 585 Processing helix chain 'B' and resid 591 through 605 removed outlier: 3.603A pdb=" N ASP B 598 " --> pdb=" O THR B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 643 removed outlier: 4.052A pdb=" N ILE B 631 " --> pdb=" O GLY B 627 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS B 643 " --> pdb=" O LYS B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 757 Processing helix chain 'B' and resid 761 through 766 Processing helix chain 'B' and resid 774 through 810 removed outlier: 3.857A pdb=" N VAL B 786 " --> pdb=" O THR B 782 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG B 787 " --> pdb=" O ALA B 783 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET B 788 " --> pdb=" O ARG B 784 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N HIS B 790 " --> pdb=" O VAL B 786 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N SER B 791 " --> pdb=" O ARG B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 820 removed outlier: 3.804A pdb=" N VAL B 818 " --> pdb=" O SER B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 835 removed outlier: 3.560A pdb=" N TRP B 830 " --> pdb=" O LEU B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 855 removed outlier: 3.738A pdb=" N ASN B 851 " --> pdb=" O ASN B 847 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG B 852 " --> pdb=" O TYR B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 885 removed outlier: 3.501A pdb=" N LYS B 885 " --> pdb=" O SER B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 916 Processing helix chain 'B' and resid 933 through 947 removed outlier: 4.067A pdb=" N ILE B 937 " --> pdb=" O GLY B 933 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ASP B 938 " --> pdb=" O ASN B 934 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASN B 939 " --> pdb=" O GLU B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 971 Processing helix chain 'B' and resid 972 through 992 Processing helix chain 'B' and resid 1003 through 1016 removed outlier: 3.912A pdb=" N TRP B1008 " --> pdb=" O ASP B1004 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL B1009 " --> pdb=" O ILE B1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 1041 through 1046 Processing helix chain 'B' and resid 1087 through 1105 removed outlier: 4.352A pdb=" N PHE B1104 " --> pdb=" O ASN B1100 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS B1105 " --> pdb=" O GLU B1101 " (cutoff:3.500A) Processing helix chain 'B' and resid 1109 through 1117 removed outlier: 3.529A pdb=" N ARG B1116 " --> pdb=" O ARG B1112 " (cutoff:3.500A) Processing helix chain 'B' and resid 1122 through 1136 Processing helix chain 'B' and resid 1143 through 1145 No H-bonds generated for 'chain 'B' and resid 1143 through 1145' Processing helix chain 'C' and resid 128 through 141 Processing helix chain 'C' and resid 143 through 156 removed outlier: 3.818A pdb=" N VAL C 154 " --> pdb=" O LEU C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 175 removed outlier: 4.974A pdb=" N THR C 167 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASP C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 190 removed outlier: 3.830A pdb=" N ALA C 188 " --> pdb=" O SER C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 198 through 209 Processing helix chain 'C' and resid 211 through 226 Processing helix chain 'C' and resid 229 through 244 removed outlier: 3.909A pdb=" N ILE C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU C 239 " --> pdb=" O ARG C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 260 removed outlier: 4.027A pdb=" N ALA C 249 " --> pdb=" O GLN C 245 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASP C 251 " --> pdb=" O ALA C 247 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY C 252 " --> pdb=" O ARG C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 277 removed outlier: 3.509A pdb=" N LEU C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 311 removed outlier: 3.538A pdb=" N LYS C 289 " --> pdb=" O GLU C 285 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 338 Processing helix chain 'C' and resid 342 through 350 Processing helix chain 'C' and resid 356 through 371 removed outlier: 4.527A pdb=" N ILE C 362 " --> pdb=" O SER C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 389 removed outlier: 3.588A pdb=" N GLN C 389 " --> pdb=" O ALA C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 399 Processing helix chain 'C' and resid 403 through 412 removed outlier: 6.178A pdb=" N ASN C 408 " --> pdb=" O GLU C 405 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ARG C 409 " --> pdb=" O PHE C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 420 through 426 Processing helix chain 'C' and resid 431 through 445 Processing helix chain 'C' and resid 447 through 456 Processing helix chain 'C' and resid 457 through 460 Processing helix chain 'C' and resid 462 through 465 Processing helix chain 'C' and resid 466 through 480 Processing helix chain 'C' and resid 482 through 491 Processing helix chain 'C' and resid 492 through 496 Processing helix chain 'C' and resid 501 through 516 Proline residue: C 507 - end of helix Processing helix chain 'C' and resid 517 through 532 Processing helix chain 'C' and resid 535 through 549 Processing helix chain 'C' and resid 551 through 576 Processing helix chain 'C' and resid 614 through 639 removed outlier: 4.406A pdb=" N GLU C 619 " --> pdb=" O ARG C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 666 removed outlier: 3.914A pdb=" N GLU C 659 " --> pdb=" O ASN C 655 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 660 " --> pdb=" O THR C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 750 Processing helix chain 'C' and resid 751 through 765 Processing helix chain 'C' and resid 765 through 770 Processing helix chain 'C' and resid 771 through 787 Processing helix chain 'C' and resid 791 through 806 Processing helix chain 'C' and resid 809 through 819 Processing helix chain 'C' and resid 822 through 832 removed outlier: 4.127A pdb=" N SER C 826 " --> pdb=" O ARG C 822 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE C 829 " --> pdb=" O SER C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 852 Processing helix chain 'C' and resid 874 through 887 Processing helix chain 'C' and resid 890 through 903 Processing helix chain 'C' and resid 908 through 924 Processing helix chain 'C' and resid 930 through 953 removed outlier: 3.747A pdb=" N TYR C 953 " --> pdb=" O ARG C 949 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 973 Processing helix chain 'C' and resid 974 through 988 removed outlier: 4.185A pdb=" N GLU C 980 " --> pdb=" O SER C 976 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR C 981 " --> pdb=" O ILE C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 1009 removed outlier: 4.227A pdb=" N HIS C 997 " --> pdb=" O LYS C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1011 through 1023 Processing helix chain 'D' and resid 48 through 59 removed outlier: 3.822A pdb=" N CYS D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 69 Processing helix chain 'D' and resid 124 through 129 removed outlier: 3.908A pdb=" N LYS D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 139 Processing helix chain 'D' and resid 173 through 181 Processing helix chain 'D' and resid 187 through 198 Processing helix chain 'D' and resid 208 through 212 Processing helix chain 'D' and resid 612 through 616 Processing helix chain 'D' and resid 617 through 629 removed outlier: 4.262A pdb=" N LEU D 628 " --> pdb=" O LYS D 624 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 640 removed outlier: 3.549A pdb=" N ALA D 633 " --> pdb=" O ASP D 629 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 163 Processing helix chain 'E' and resid 165 through 175 Processing helix chain 'E' and resid 177 through 192 removed outlier: 4.218A pdb=" N LEU E 183 " --> pdb=" O GLU E 179 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU E 184 " --> pdb=" O LYS E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 204 removed outlier: 4.119A pdb=" N ILE E 203 " --> pdb=" O PRO E 199 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN E 204 " --> pdb=" O PHE E 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 199 through 204' Processing helix chain 'E' and resid 215 through 219 Processing helix chain 'E' and resid 222 through 227 Processing helix chain 'E' and resid 228 through 232 removed outlier: 4.031A pdb=" N ARG E 232 " --> pdb=" O ASP E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 247 Processing helix chain 'E' and resid 326 through 330 removed outlier: 3.503A pdb=" N LEU E 329 " --> pdb=" O ASN E 326 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU E 330 " --> pdb=" O GLU E 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 326 through 330' Processing helix chain 'E' and resid 498 through 503 Processing helix chain 'E' and resid 582 through 587 Processing helix chain 'E' and resid 592 through 597 removed outlier: 3.861A pdb=" N GLN E 597 " --> pdb=" O SER E 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 637 through 640 Processing helix chain 'F' and resid 51 through 54 Processing helix chain 'F' and resid 306 through 322 removed outlier: 3.617A pdb=" N LEU F 310 " --> pdb=" O ILE F 306 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE F 320 " --> pdb=" O LYS F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 363 Processing helix chain 'F' and resid 385 through 395 removed outlier: 4.127A pdb=" N TYR F 389 " --> pdb=" O GLY F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 433 Processing helix chain 'F' and resid 433 through 444 removed outlier: 3.839A pdb=" N MET F 444 " --> pdb=" O MET F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 465 removed outlier: 3.750A pdb=" N ALA F 457 " --> pdb=" O SER F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 469 Processing helix chain 'F' and resid 471 through 486 Processing helix chain 'F' and resid 510 through 512 No H-bonds generated for 'chain 'F' and resid 510 through 512' Processing helix chain 'F' and resid 564 through 574 Processing helix chain 'G' and resid 14 through 18 removed outlier: 3.616A pdb=" N LEU G 18 " --> pdb=" O SER G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 54 removed outlier: 3.826A pdb=" N LYS G 45 " --> pdb=" O VAL G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 81 Proline residue: G 75 - end of helix Processing helix chain 'G' and resid 88 through 91 Processing helix chain 'G' and resid 107 through 115 removed outlier: 4.254A pdb=" N LYS G 113 " --> pdb=" O GLU G 109 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE G 114 " --> pdb=" O ILE G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 158 removed outlier: 3.521A pdb=" N TRP G 147 " --> pdb=" O PHE G 143 " (cutoff:3.500A) Proline residue: G 148 - end of helix removed outlier: 3.723A pdb=" N GLU G 152 " --> pdb=" O PRO G 148 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS G 156 " --> pdb=" O GLU G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 182 Processing helix chain 'G' and resid 351 through 354 Processing helix chain 'H' and resid 178 through 190 Processing helix chain 'H' and resid 194 through 212 Processing helix chain 'H' and resid 219 through 235 Processing helix chain 'H' and resid 240 through 248 removed outlier: 3.638A pdb=" N ILE H 244 " --> pdb=" O THR H 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 265 Processing helix chain 'H' and resid 267 through 272 Processing helix chain 'H' and resid 287 through 297 removed outlier: 4.816A pdb=" N ASN H 293 " --> pdb=" O SER H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 407 through 413 Processing helix chain 'H' and resid 454 through 472 removed outlier: 3.567A pdb=" N LYS H 459 " --> pdb=" O GLU H 455 " (cutoff:3.500A) Processing helix chain 'H' and resid 497 through 505 Processing helix chain 'H' and resid 545 through 563 removed outlier: 4.034A pdb=" N ILE H 549 " --> pdb=" O GLN H 545 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR H 550 " --> pdb=" O ARG H 546 " (cutoff:3.500A) Proline residue: H 558 - end of helix removed outlier: 3.631A pdb=" N PHE H 563 " --> pdb=" O VAL H 559 " (cutoff:3.500A) Processing helix chain 'H' and resid 587 through 593 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 109 Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 135 Processing sheet with id=AA4, first strand: chain 'A' and resid 194 through 195 Processing sheet with id=AA5, first strand: chain 'A' and resid 221 through 223 Processing sheet with id=AA6, first strand: chain 'A' and resid 249 through 251 removed outlier: 4.163A pdb=" N PHE D 643 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ASN B 994 " --> pdb=" O ALA B1053 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ALA B1053 " --> pdb=" O ASN B 994 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AA8, first strand: chain 'B' and resid 24 through 26 Processing sheet with id=AA9, first strand: chain 'B' and resid 125 through 126 removed outlier: 3.584A pdb=" N SER B 155 " --> pdb=" O GLN B 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 203 through 205 removed outlier: 6.203A pdb=" N ILE B 251 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 350 through 351 removed outlier: 6.473A pdb=" N GLU B 377 " --> pdb=" O ARG B 393 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N TYR B 395 " --> pdb=" O GLU B 377 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 454 through 457 Processing sheet with id=AB4, first strand: chain 'B' and resid 569 through 571 Processing sheet with id=AB5, first strand: chain 'B' and resid 655 through 656 Processing sheet with id=AB6, first strand: chain 'B' and resid 858 through 859 removed outlier: 4.936A pdb=" N LEU G 335 " --> pdb=" O VAL G 432 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG G 334 " --> pdb=" O ILE G 331 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 888 through 892 removed outlier: 6.917A pdb=" N TRP G 340 " --> pdb=" O ILE B 891 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE D 36 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASN D 156 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE D 160 " --> pdb=" O GLU D 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 888 through 892 removed outlier: 6.917A pdb=" N TRP G 340 " --> pdb=" O ILE B 891 " (cutoff:3.500A) removed outlier: 10.835A pdb=" N LEU G 343 " --> pdb=" O ILE G 427 " (cutoff:3.500A) removed outlier: 11.325A pdb=" N ILE G 427 " --> pdb=" O LEU G 343 " (cutoff:3.500A) removed outlier: 10.687A pdb=" N GLY G 345 " --> pdb=" O GLU G 425 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLU G 425 " --> pdb=" O GLY G 345 " (cutoff:3.500A) removed outlier: 18.068A pdb=" N VAL G 291 " --> pdb=" O TYR G 421 " (cutoff:3.500A) removed outlier: 15.160A pdb=" N ILE G 423 " --> pdb=" O VAL G 291 " (cutoff:3.500A) removed outlier: 14.517A pdb=" N THR G 293 " --> pdb=" O ILE G 423 " (cutoff:3.500A) removed outlier: 11.237A pdb=" N GLU G 425 " --> pdb=" O THR G 293 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N TYR G 295 " --> pdb=" O GLU G 425 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N ILE G 427 " --> pdb=" O TYR G 295 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N SER G 297 " --> pdb=" O ILE G 427 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER D 114 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE D 153 " --> pdb=" O SER D 114 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE D 116 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG D 147 " --> pdb=" O THR D 120 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 950 through 953 Processing sheet with id=AC1, first strand: chain 'B' and resid 1139 through 1142 removed outlier: 3.757A pdb=" N GLY B1146 " --> pdb=" O THR B1142 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 726 through 727 Processing sheet with id=AC3, first strand: chain 'C' and resid 1024 through 1025 Processing sheet with id=AC4, first strand: chain 'E' and resid 234 through 238 removed outlier: 3.609A pdb=" N LYS E 413 " --> pdb=" O VAL E 234 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N HIS E 236 " --> pdb=" O CYS E 411 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N CYS E 411 " --> pdb=" O HIS E 236 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ILE E 238 " --> pdb=" O LYS E 409 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LYS E 409 " --> pdb=" O ILE E 238 " (cutoff:3.500A) removed outlier: 9.163A pdb=" N VAL E 407 " --> pdb=" O VAL E 354 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL E 356 " --> pdb=" O VAL E 407 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N LYS E 409 " --> pdb=" O VAL E 356 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N THR E 358 " --> pdb=" O LYS E 409 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N CYS E 411 " --> pdb=" O THR E 358 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N VAL E 360 " --> pdb=" O CYS E 411 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N LYS E 413 " --> pdb=" O VAL E 360 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N CYS E 353 " --> pdb=" O ASN E 347 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ASN E 347 " --> pdb=" O CYS E 353 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LYS E 355 " --> pdb=" O LYS E 345 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LYS E 345 " --> pdb=" O LYS E 355 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N TYR E 312 " --> pdb=" O TRP E 297 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N TRP E 297 " --> pdb=" O TYR E 312 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALA E 314 " --> pdb=" O ILE E 295 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE E 295 " --> pdb=" O ALA E 314 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA E 316 " --> pdb=" O THR E 293 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 261 through 265 removed outlier: 6.621A pdb=" N LYS E 255 " --> pdb=" O TYR E 614 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE E 616 " --> pdb=" O LYS E 255 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU E 257 " --> pdb=" O ILE E 616 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 271 through 272 removed outlier: 3.902A pdb=" N CYS E 644 " --> pdb=" O SER E 660 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 366 through 371 removed outlier: 5.435A pdb=" N ASP E 368 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N VAL E 387 " --> pdb=" O ASP E 368 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE E 398 " --> pdb=" O VAL E 381 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N CYS E 383 " --> pdb=" O LEU E 396 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU E 396 " --> pdb=" O CYS E 383 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N SER E 385 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ASN E 394 " --> pdb=" O SER E 385 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 425 through 432 removed outlier: 6.559A pdb=" N GLY E 439 " --> pdb=" O THR E 426 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE E 428 " --> pdb=" O VAL E 437 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL E 437 " --> pdb=" O PHE E 428 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N PHE E 430 " --> pdb=" O THR E 435 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N THR E 435 " --> pdb=" O PHE E 430 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE E 444 " --> pdb=" O PHE E 440 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 467 through 473 removed outlier: 3.585A pdb=" N SER E 469 " --> pdb=" O VAL E 485 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL E 481 " --> pdb=" O ALA E 473 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA E 486 " --> pdb=" O TYR E 490 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TYR E 490 " --> pdb=" O ALA E 486 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE E 491 " --> pdb=" O VAL E 506 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 517 through 520 removed outlier: 6.680A pdb=" N LEU E 535 " --> pdb=" O LEU E 549 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 556 through 560 removed outlier: 6.883A pdb=" N GLY E 571 " --> pdb=" O THR E 557 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE E 559 " --> pdb=" O LEU E 569 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU E 569 " --> pdb=" O ILE E 559 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER E 576 " --> pdb=" O SER E 572 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TRP E 603 " --> pdb=" O LEU E 577 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE E 579 " --> pdb=" O ARG E 601 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ARG E 601 " --> pdb=" O ILE E 579 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N ASN E 581 " --> pdb=" O SER E 599 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N SER E 599 " --> pdb=" O ASN E 581 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU E 621 " --> pdb=" O ARG E 601 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 7 through 10 removed outlier: 9.143A pdb=" N SER F 365 " --> pdb=" O MET F 351 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N MET F 351 " --> pdb=" O SER F 365 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY F 335 " --> pdb=" O VAL F 348 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASP F 350 " --> pdb=" O ILE F 333 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE F 333 " --> pdb=" O ASP F 350 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLU F 352 " --> pdb=" O LEU F 331 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LEU F 331 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 21 through 23 removed outlier: 4.230A pdb=" N ILE F 37 " --> pdb=" O PHE F 61 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 88 through 93 removed outlier: 6.495A pdb=" N LEU F 103 " --> pdb=" O ARG F 89 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N CYS F 91 " --> pdb=" O ALA F 101 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA F 101 " --> pdb=" O CYS F 91 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL F 109 " --> pdb=" O ASN F 120 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ASN F 120 " --> pdb=" O VAL F 109 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL F 111 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 132 through 137 removed outlier: 3.673A pdb=" N CYS F 134 " --> pdb=" O GLY F 147 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU F 152 " --> pdb=" O ASN F 148 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER F 172 " --> pdb=" O PHE F 155 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N SER F 157 " --> pdb=" O PHE F 170 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N PHE F 170 " --> pdb=" O SER F 157 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ARG F 159 " --> pdb=" O PHE F 168 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N PHE F 168 " --> pdb=" O ARG F 159 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 185 through 191 removed outlier: 6.803A pdb=" N ALA F 198 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE F 188 " --> pdb=" O VAL F 196 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL F 196 " --> pdb=" O ILE F 188 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TRP F 190 " --> pdb=" O VAL F 194 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL F 194 " --> pdb=" O TRP F 190 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL F 204 " --> pdb=" O ILE F 221 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG F 219 " --> pdb=" O SER F 206 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 231 through 235 removed outlier: 3.731A pdb=" N ASP F 231 " --> pdb=" O THR F 242 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 269 through 272 Processing sheet with id=AE1, first strand: chain 'F' and resid 495 through 499 Processing sheet with id=AE2, first strand: chain 'F' and resid 518 through 520 Processing sheet with id=AE3, first strand: chain 'F' and resid 542 through 544 Processing sheet with id=AE4, first strand: chain 'G' and resid 119 through 120 removed outlier: 6.646A pdb=" N VAL G 84 " --> pdb=" O SER G 120 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA G 61 " --> pdb=" O TYR G 85 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA G 60 " --> pdb=" O CYS G 163 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU G 204 " --> pdb=" O ASN G 241 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASN G 241 " --> pdb=" O LEU G 204 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LYS G 206 " --> pdb=" O THR G 239 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 419 through 421 removed outlier: 4.768A pdb=" N ASN H 421 " --> pdb=" O ALA H 427 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ALA H 427 " --> pdb=" O ASN H 421 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL H 428 " --> pdb=" O ILE H 441 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE H 441 " --> pdb=" O VAL H 428 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS H 446 " --> pdb=" O PHE H 442 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY H 451 " --> pdb=" O ILE H 396 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ILE H 396 " --> pdb=" O GLY H 451 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU H 393 " --> pdb=" O VAL H 487 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL H 487 " --> pdb=" O LEU H 393 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ASN H 395 " --> pdb=" O ASN H 485 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASN H 485 " --> pdb=" O ASN H 395 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL H 397 " --> pdb=" O ILE H 483 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ILE H 483 " --> pdb=" O VAL H 397 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR H 399 " --> pdb=" O PHE H 481 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N PHE H 481 " --> pdb=" O THR H 399 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ILE H 486 " --> pdb=" O GLY H 542 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY H 542 " --> pdb=" O ILE H 486 " (cutoff:3.500A) 1503 hydrogen bonds defined for protein. 4251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 275 hydrogen bonds 542 hydrogen bond angles 0 basepair planarities 111 basepair parallelities 240 stacking parallelities Total time for adding SS restraints: 21.04 Time building geometry restraints manager: 18.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9995 1.34 - 1.46: 9277 1.46 - 1.58: 20287 1.58 - 1.71: 602 1.71 - 1.83: 221 Bond restraints: 40382 Sorted by residual: bond pdb=" CA PRO H 287 " pdb=" C PRO H 287 " ideal model delta sigma weight residual 1.517 1.544 -0.027 6.70e-03 2.23e+04 1.63e+01 bond pdb=" CZ ARG A 97 " pdb=" NH2 ARG A 97 " ideal model delta sigma weight residual 1.330 1.283 0.047 1.30e-02 5.92e+03 1.32e+01 bond pdb=" CZ ARG C 967 " pdb=" NH2 ARG C 967 " ideal model delta sigma weight residual 1.330 1.285 0.045 1.30e-02 5.92e+03 1.18e+01 bond pdb=" CZ ARG F 89 " pdb=" NH2 ARG F 89 " ideal model delta sigma weight residual 1.330 1.287 0.043 1.30e-02 5.92e+03 1.09e+01 bond pdb=" CZ ARG E 508 " pdb=" NH2 ARG E 508 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.07e+01 ... (remaining 40377 not shown) Histogram of bond angle deviations from ideal: 97.82 - 105.47: 1961 105.47 - 113.13: 20251 113.13 - 120.79: 20595 120.79 - 128.45: 12558 128.45 - 136.11: 512 Bond angle restraints: 55877 Sorted by residual: angle pdb=" N ALA C 724 " pdb=" CA ALA C 724 " pdb=" C ALA C 724 " ideal model delta sigma weight residual 111.07 119.37 -8.30 1.07e+00 8.73e-01 6.01e+01 angle pdb=" N CYS C 821 " pdb=" CA CYS C 821 " pdb=" C CYS C 821 " ideal model delta sigma weight residual 111.71 119.73 -8.02 1.15e+00 7.56e-01 4.87e+01 angle pdb=" N GLY E 279 " pdb=" CA GLY E 279 " pdb=" C GLY E 279 " ideal model delta sigma weight residual 111.63 119.38 -7.75 1.15e+00 7.56e-01 4.54e+01 angle pdb=" N ASP A 187 " pdb=" CA ASP A 187 " pdb=" C ASP A 187 " ideal model delta sigma weight residual 110.08 119.34 -9.26 1.38e+00 5.25e-01 4.51e+01 angle pdb=" N PHE F 423 " pdb=" CA PHE F 423 " pdb=" C PHE F 423 " ideal model delta sigma weight residual 111.11 118.97 -7.86 1.20e+00 6.94e-01 4.29e+01 ... (remaining 55872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 22345 35.87 - 71.74: 1238 71.74 - 107.60: 44 107.60 - 143.47: 0 143.47 - 179.34: 9 Dihedral angle restraints: 23636 sinusoidal: 11703 harmonic: 11933 Sorted by residual: dihedral pdb=" C ASP A 281 " pdb=" N ASP A 281 " pdb=" CA ASP A 281 " pdb=" CB ASP A 281 " ideal model delta harmonic sigma weight residual -122.60 -138.75 16.15 0 2.50e+00 1.60e-01 4.17e+01 dihedral pdb=" N ASP A 281 " pdb=" C ASP A 281 " pdb=" CA ASP A 281 " pdb=" CB ASP A 281 " ideal model delta harmonic sigma weight residual 122.80 136.92 -14.12 0 2.50e+00 1.60e-01 3.19e+01 dihedral pdb=" C PHE H 275 " pdb=" N PHE H 275 " pdb=" CA PHE H 275 " pdb=" CB PHE H 275 " ideal model delta harmonic sigma weight residual -122.60 -136.51 13.91 0 2.50e+00 1.60e-01 3.10e+01 ... (remaining 23633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 4961 0.116 - 0.232: 1137 0.232 - 0.348: 121 0.348 - 0.463: 28 0.463 - 0.579: 3 Chirality restraints: 6250 Sorted by residual: chirality pdb=" CA ASP A 281 " pdb=" N ASP A 281 " pdb=" C ASP A 281 " pdb=" CB ASP A 281 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.39e+00 chirality pdb=" CA PHE H 275 " pdb=" N PHE H 275 " pdb=" C PHE H 275 " pdb=" CB PHE H 275 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.96e+00 chirality pdb=" CA THR C 722 " pdb=" N THR C 722 " pdb=" C THR C 722 " pdb=" CB THR C 722 " both_signs ideal model delta sigma weight residual False 2.53 2.00 0.52 2.00e-01 2.50e+01 6.85e+00 ... (remaining 6247 not shown) Planarity restraints: 6036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 97 " 0.240 2.00e-02 2.50e+03 9.99e-02 2.99e+02 pdb=" N9 DG I 97 " -0.027 2.00e-02 2.50e+03 pdb=" C8 DG I 97 " -0.071 2.00e-02 2.50e+03 pdb=" N7 DG I 97 " -0.076 2.00e-02 2.50e+03 pdb=" C5 DG I 97 " -0.063 2.00e-02 2.50e+03 pdb=" C6 DG I 97 " 0.018 2.00e-02 2.50e+03 pdb=" O6 DG I 97 " 0.174 2.00e-02 2.50e+03 pdb=" N1 DG I 97 " 0.017 2.00e-02 2.50e+03 pdb=" C2 DG I 97 " -0.043 2.00e-02 2.50e+03 pdb=" N2 DG I 97 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 97 " -0.081 2.00e-02 2.50e+03 pdb=" C4 DG I 97 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 963 " 0.204 2.00e-02 2.50e+03 1.13e-01 2.53e+02 pdb=" CG TYR C 963 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR C 963 " -0.099 2.00e-02 2.50e+03 pdb=" CD2 TYR C 963 " -0.096 2.00e-02 2.50e+03 pdb=" CE1 TYR C 963 " -0.066 2.00e-02 2.50e+03 pdb=" CE2 TYR C 963 " -0.069 2.00e-02 2.50e+03 pdb=" CZ TYR C 963 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR C 963 " 0.170 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 66 " -0.201 2.00e-02 2.50e+03 1.03e-01 2.38e+02 pdb=" N1 DC I 66 " 0.026 2.00e-02 2.50e+03 pdb=" C2 DC I 66 " 0.054 2.00e-02 2.50e+03 pdb=" O2 DC I 66 " 0.077 2.00e-02 2.50e+03 pdb=" N3 DC I 66 " 0.020 2.00e-02 2.50e+03 pdb=" C4 DC I 66 " 0.003 2.00e-02 2.50e+03 pdb=" N4 DC I 66 " -0.165 2.00e-02 2.50e+03 pdb=" C5 DC I 66 " 0.097 2.00e-02 2.50e+03 pdb=" C6 DC I 66 " 0.091 2.00e-02 2.50e+03 ... (remaining 6033 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 18186 3.00 - 3.48: 40020 3.48 - 3.95: 64574 3.95 - 4.43: 72855 4.43 - 4.90: 113666 Nonbonded interactions: 309301 Sorted by model distance: nonbonded pdb=" OG SER A 111 " pdb=" OE2 GLU A 127 " model vdw 2.526 2.440 nonbonded pdb=" OE1 GLU H 216 " pdb=" OH TYR H 511 " model vdw 2.544 2.440 nonbonded pdb=" OG SER E 318 " pdb=" OE2 GLU E 365 " model vdw 2.545 2.440 nonbonded pdb=" OG SER F 339 " pdb=" OD1 ASP F 341 " model vdw 2.547 2.440 nonbonded pdb=" OG SER F 128 " pdb=" OD1 ASP F 150 " model vdw 2.547 2.440 ... (remaining 309296 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.610 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: 0.110 Extract box with map and model: 15.320 Check model and map are aligned: 0.590 Set scattering table: 0.390 Process input model: 123.190 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.120 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 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 : 0.013 0.047 40382 Z= 0.799 Angle : 1.890 9.848 55877 Z= 1.262 Chirality : 0.099 0.579 6250 Planarity : 0.018 0.211 6036 Dihedral : 18.551 179.340 15882 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 0.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.50 % Favored : 94.38 % Rotamer: Outliers : 0.38 % Allowed : 2.81 % Favored : 96.81 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.12), residues: 3985 helix: -0.59 (0.11), residues: 1618 sheet: -0.44 (0.22), residues: 504 loop : -0.85 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.122 0.023 TRP E 603 HIS 0.019 0.004 HIS E 337 PHE 0.094 0.015 PHE F 324 TYR 0.204 0.023 TYR C 963 ARG 0.017 0.001 ARG E 552 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 502 time to evaluate : 4.223 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: A 382 TYR cc_start: 0.3148 (t80) cc_final: 0.2892 (t80) REVERT: B 415 LEU cc_start: 0.7868 (mm) cc_final: 0.7625 (pp) REVERT: C 228 MET cc_start: 0.4886 (tmm) cc_final: 0.4291 (tmm) REVERT: C 265 ASN cc_start: 0.6745 (m-40) cc_final: 0.5982 (t0) REVERT: C 506 LYS cc_start: 0.5321 (mtmt) cc_final: 0.4673 (tptm) REVERT: C 814 GLN cc_start: 0.8333 (mt0) cc_final: 0.8042 (mt0) REVERT: F 270 ILE cc_start: 0.8688 (mt) cc_final: 0.8272 (mt) REVERT: F 343 TYR cc_start: 0.8335 (m-80) cc_final: 0.8106 (m-80) REVERT: G 139 MET cc_start: 0.7688 (ttp) cc_final: 0.7392 (ttp) REVERT: H 234 MET cc_start: 0.2390 (mmm) cc_final: 0.1548 (mmm) outliers start: 14 outliers final: 2 residues processed: 512 average time/residue: 0.5527 time to fit residues: 458.8739 Evaluate side-chains 244 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 242 time to evaluate : 4.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain E residue 420 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 363 optimal weight: 0.9980 chunk 325 optimal weight: 1.9990 chunk 180 optimal weight: 0.7980 chunk 111 optimal weight: 7.9990 chunk 219 optimal weight: 0.7980 chunk 174 optimal weight: 0.7980 chunk 337 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 204 optimal weight: 1.9990 chunk 250 optimal weight: 3.9990 chunk 390 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 HIS A 359 ASN B 201 ASN C 161 ASN C 190 HIS C 836 GLN C 930 GLN F 525 ASN G 56 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 40382 Z= 0.223 Angle : 0.678 10.139 55877 Z= 0.382 Chirality : 0.045 0.323 6250 Planarity : 0.004 0.055 6036 Dihedral : 22.677 178.923 7707 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.81 % Favored : 97.16 % Rotamer: Outliers : 1.06 % Allowed : 6.85 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 0.11 (0.13), residues: 3985 helix: 0.98 (0.12), residues: 1652 sheet: -0.53 (0.20), residues: 608 loop : -0.50 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 184 HIS 0.010 0.001 HIS A 159 PHE 0.033 0.002 PHE E 273 TYR 0.022 0.002 TYR F 169 ARG 0.006 0.001 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 260 time to evaluate : 4.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 MET cc_start: 0.7864 (tpp) cc_final: 0.7650 (tpp) REVERT: B 132 GLN cc_start: 0.6615 (pt0) cc_final: 0.6358 (mt0) REVERT: B 415 LEU cc_start: 0.7679 (mm) cc_final: 0.7182 (pp) REVERT: B 999 ASN cc_start: 0.7271 (t0) cc_final: 0.7067 (t0) REVERT: B 1160 THR cc_start: 0.2720 (OUTLIER) cc_final: 0.2505 (m) REVERT: C 265 ASN cc_start: 0.6505 (m-40) cc_final: 0.5369 (t0) REVERT: C 387 TRP cc_start: 0.4468 (t-100) cc_final: 0.4242 (t-100) REVERT: F 343 TYR cc_start: 0.8421 (m-80) cc_final: 0.8097 (m-80) REVERT: G 1 MET cc_start: 0.3280 (mtm) cc_final: 0.2641 (mtm) REVERT: H 234 MET cc_start: 0.2089 (mmm) cc_final: 0.1448 (mmm) outliers start: 39 outliers final: 21 residues processed: 290 average time/residue: 0.4691 time to fit residues: 232.1372 Evaluate side-chains 213 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 191 time to evaluate : 4.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 1004 ASP Chi-restraints excluded: chain B residue 1160 THR Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 188 LYS Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 379 HIS Chi-restraints excluded: chain E residue 476 ASP Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 593 SER Chi-restraints excluded: chain E residue 616 ILE Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 351 MET Chi-restraints excluded: chain F residue 583 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 244 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 217 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 324 optimal weight: 6.9990 chunk 265 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 391 optimal weight: 10.0000 chunk 422 optimal weight: 20.0000 chunk 348 optimal weight: 3.9990 chunk 387 optimal weight: 50.0000 chunk 133 optimal weight: 9.9990 chunk 313 optimal weight: 4.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 HIS ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 HIS ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN F 364 GLN F 575 ASN H 241 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 40382 Z= 0.360 Angle : 0.698 13.557 55877 Z= 0.383 Chirality : 0.045 0.306 6250 Planarity : 0.005 0.057 6036 Dihedral : 22.858 177.346 7704 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.94 % Allowed : 8.27 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 0.03 (0.13), residues: 3985 helix: 1.09 (0.12), residues: 1658 sheet: -0.50 (0.21), residues: 565 loop : -0.77 (0.15), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 830 HIS 0.008 0.002 HIS G 169 PHE 0.023 0.002 PHE C 846 TYR 0.035 0.002 TYR B 951 ARG 0.023 0.001 ARG B 748 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 200 time to evaluate : 4.282 Fit side-chains REVERT: A 246 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7415 (t0) REVERT: B 302 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.7018 (p90) REVERT: B 329 ASN cc_start: 0.7778 (OUTLIER) cc_final: 0.7468 (t0) REVERT: B 458 ASP cc_start: 0.7379 (p0) cc_final: 0.6892 (t0) REVERT: B 583 TYR cc_start: 0.4350 (m-80) cc_final: 0.4141 (m-80) REVERT: B 999 ASN cc_start: 0.7559 (t0) cc_final: 0.7348 (t0) REVERT: C 217 TYR cc_start: 0.0753 (OUTLIER) cc_final: 0.0088 (m-80) REVERT: C 229 GLU cc_start: 0.7278 (mm-30) cc_final: 0.6703 (mp0) REVERT: C 720 THR cc_start: 0.7251 (m) cc_final: 0.6994 (p) REVERT: F 588 MET cc_start: 0.5577 (ptp) cc_final: 0.5170 (ptp) REVERT: H 234 MET cc_start: 0.1991 (mmm) cc_final: 0.0887 (ppp) outliers start: 71 outliers final: 43 residues processed: 258 average time/residue: 0.4586 time to fit residues: 204.7506 Evaluate side-chains 223 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 176 time to evaluate : 4.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 302 PHE Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 886 THR Chi-restraints excluded: chain B residue 1004 ASP Chi-restraints excluded: chain B residue 1110 LEU Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 965 LEU Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 379 HIS Chi-restraints excluded: chain E residue 467 ILE Chi-restraints excluded: chain E residue 470 VAL Chi-restraints excluded: chain E residue 476 ASP Chi-restraints excluded: chain E residue 525 SER Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 578 ILE Chi-restraints excluded: chain E residue 593 SER Chi-restraints excluded: chain E residue 616 ILE Chi-restraints excluded: chain E residue 640 ILE Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 184 TRP Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 351 MET Chi-restraints excluded: chain F residue 366 PHE Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain H residue 214 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 386 optimal weight: 40.0000 chunk 294 optimal weight: 4.9990 chunk 203 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 186 optimal weight: 0.8980 chunk 262 optimal weight: 0.8980 chunk 392 optimal weight: 40.0000 chunk 415 optimal weight: 10.0000 chunk 205 optimal weight: 2.9990 chunk 372 optimal weight: 30.0000 chunk 112 optimal weight: 7.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN G 243 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 40382 Z= 0.247 Angle : 0.595 10.618 55877 Z= 0.330 Chirality : 0.041 0.219 6250 Planarity : 0.004 0.057 6036 Dihedral : 22.802 175.940 7704 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.77 % Allowed : 9.94 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 3985 helix: 1.36 (0.13), residues: 1669 sheet: -0.62 (0.21), residues: 580 loop : -0.73 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 830 HIS 0.007 0.001 HIS G 169 PHE 0.018 0.002 PHE F 441 TYR 0.023 0.002 TYR B 395 ARG 0.005 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 190 time to evaluate : 4.415 Fit side-chains REVERT: B 329 ASN cc_start: 0.7874 (OUTLIER) cc_final: 0.7493 (t0) REVERT: B 458 ASP cc_start: 0.7592 (p0) cc_final: 0.6875 (t0) REVERT: B 583 TYR cc_start: 0.4556 (m-80) cc_final: 0.4341 (m-80) REVERT: B 999 ASN cc_start: 0.7496 (t0) cc_final: 0.7258 (t0) REVERT: C 217 TYR cc_start: 0.0744 (OUTLIER) cc_final: 0.0058 (m-80) REVERT: C 229 GLU cc_start: 0.7351 (mm-30) cc_final: 0.6737 (mp0) REVERT: C 253 PHE cc_start: 0.3502 (m-80) cc_final: 0.3123 (m-80) REVERT: C 720 THR cc_start: 0.7147 (m) cc_final: 0.6921 (p) REVERT: E 567 MET cc_start: 0.8725 (mmm) cc_final: 0.8204 (mmm) REVERT: G 169 HIS cc_start: 0.6854 (OUTLIER) cc_final: 0.5534 (m-70) REVERT: H 234 MET cc_start: 0.1929 (mmm) cc_final: 0.0789 (ppp) outliers start: 65 outliers final: 42 residues processed: 245 average time/residue: 0.4551 time to fit residues: 194.9728 Evaluate side-chains 215 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 170 time to evaluate : 3.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 886 THR Chi-restraints excluded: chain B residue 1004 ASP Chi-restraints excluded: chain B residue 1110 LEU Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 198 PHE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 308 LYS Chi-restraints excluded: chain E residue 379 HIS Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 550 VAL Chi-restraints excluded: chain E residue 593 SER Chi-restraints excluded: chain E residue 616 ILE Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 184 TRP Chi-restraints excluded: chain F residue 304 ASN Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 351 MET Chi-restraints excluded: chain F residue 366 PHE Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain H residue 214 MET Chi-restraints excluded: chain H residue 448 VAL Chi-restraints excluded: chain H residue 492 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 346 optimal weight: 1.9990 chunk 235 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 309 optimal weight: 10.0000 chunk 171 optimal weight: 1.9990 chunk 354 optimal weight: 2.9990 chunk 287 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 212 optimal weight: 1.9990 chunk 373 optimal weight: 30.0000 chunk 104 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 HIS ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 40382 Z= 0.237 Angle : 0.580 10.279 55877 Z= 0.320 Chirality : 0.040 0.184 6250 Planarity : 0.004 0.057 6036 Dihedral : 22.801 175.329 7704 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.18 % Allowed : 10.65 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 3985 helix: 1.49 (0.13), residues: 1662 sheet: -0.69 (0.21), residues: 582 loop : -0.72 (0.15), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 830 HIS 0.006 0.001 HIS G 169 PHE 0.021 0.002 PHE C 396 TYR 0.019 0.001 TYR B 332 ARG 0.003 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 175 time to evaluate : 4.564 Fit side-chains revert: symmetry clash REVERT: B 302 PHE cc_start: 0.7272 (OUTLIER) cc_final: 0.6845 (p90) REVERT: B 458 ASP cc_start: 0.7596 (p0) cc_final: 0.6840 (t0) REVERT: B 583 TYR cc_start: 0.4502 (m-80) cc_final: 0.4248 (m-80) REVERT: B 999 ASN cc_start: 0.7440 (t0) cc_final: 0.7174 (t0) REVERT: C 217 TYR cc_start: 0.0589 (OUTLIER) cc_final: 0.0069 (m-80) REVERT: C 229 GLU cc_start: 0.7430 (mm-30) cc_final: 0.6735 (mp0) REVERT: C 836 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8076 (tm130) REVERT: E 567 MET cc_start: 0.8675 (mmm) cc_final: 0.8156 (mmm) REVERT: G 169 HIS cc_start: 0.6846 (OUTLIER) cc_final: 0.5495 (m-70) REVERT: H 234 MET cc_start: 0.1875 (mmm) cc_final: 0.0769 (ppp) outliers start: 80 outliers final: 61 residues processed: 242 average time/residue: 0.4682 time to fit residues: 196.4585 Evaluate side-chains 224 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 159 time to evaluate : 4.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 81 HIS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 302 PHE Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 763 ASP Chi-restraints excluded: chain B residue 1004 ASP Chi-restraints excluded: chain B residue 1110 LEU Chi-restraints excluded: chain C residue 198 PHE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 836 GLN Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 965 LEU Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 308 LYS Chi-restraints excluded: chain E residue 379 HIS Chi-restraints excluded: chain E residue 467 ILE Chi-restraints excluded: chain E residue 470 VAL Chi-restraints excluded: chain E residue 476 ASP Chi-restraints excluded: chain E residue 525 SER Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 550 VAL Chi-restraints excluded: chain E residue 616 ILE Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 184 TRP Chi-restraints excluded: chain F residue 304 ASN Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 351 MET Chi-restraints excluded: chain F residue 366 PHE Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain H residue 214 MET Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 448 VAL Chi-restraints excluded: chain H residue 492 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 139 optimal weight: 20.0000 chunk 374 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 244 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 chunk 416 optimal weight: 10.0000 chunk 345 optimal weight: 20.0000 chunk 192 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 218 optimal weight: 2.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 HIS E 347 ASN H 394 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 40382 Z= 0.382 Angle : 0.672 10.481 55877 Z= 0.366 Chirality : 0.044 0.192 6250 Planarity : 0.005 0.059 6036 Dihedral : 23.001 174.116 7704 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.76 % Allowed : 11.11 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: -0.13 (0.13), residues: 3985 helix: 1.15 (0.13), residues: 1662 sheet: -0.88 (0.21), residues: 573 loop : -0.99 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP B 830 HIS 0.007 0.001 HIS B1105 PHE 0.024 0.002 PHE E 344 TYR 0.022 0.002 TYR B 389 ARG 0.006 0.001 ARG B 748 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 163 time to evaluate : 4.426 Fit side-chains revert: symmetry clash REVERT: B 302 PHE cc_start: 0.7348 (OUTLIER) cc_final: 0.6819 (p90) REVERT: C 217 TYR cc_start: 0.0958 (OUTLIER) cc_final: 0.0038 (m-80) REVERT: C 229 GLU cc_start: 0.7394 (mm-30) cc_final: 0.6392 (mp0) REVERT: C 287 TYR cc_start: 0.6589 (OUTLIER) cc_final: 0.4935 (m-80) REVERT: C 836 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8144 (tm130) REVERT: E 248 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7522 (mttp) REVERT: E 385 SER cc_start: 0.8321 (OUTLIER) cc_final: 0.8079 (m) REVERT: E 412 GLU cc_start: 0.6860 (mp0) cc_final: 0.6569 (mp0) REVERT: E 567 MET cc_start: 0.8819 (mmm) cc_final: 0.8148 (mmm) REVERT: G 169 HIS cc_start: 0.7102 (OUTLIER) cc_final: 0.5464 (m-70) REVERT: H 234 MET cc_start: 0.1687 (mmm) cc_final: 0.0821 (ppp) outliers start: 101 outliers final: 70 residues processed: 250 average time/residue: 0.4764 time to fit residues: 207.0792 Evaluate side-chains 225 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 148 time to evaluate : 4.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 81 HIS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 302 PHE Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 763 ASP Chi-restraints excluded: chain B residue 1004 ASP Chi-restraints excluded: chain B residue 1101 GLU Chi-restraints excluded: chain B residue 1110 LEU Chi-restraints excluded: chain C residue 198 PHE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 287 TYR Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 433 ASP Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 624 ILE Chi-restraints excluded: chain C residue 836 GLN Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 965 LEU Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 308 LYS Chi-restraints excluded: chain E residue 379 HIS Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 467 ILE Chi-restraints excluded: chain E residue 470 VAL Chi-restraints excluded: chain E residue 476 ASP Chi-restraints excluded: chain E residue 525 SER Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 578 ILE Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 593 SER Chi-restraints excluded: chain E residue 616 ILE Chi-restraints excluded: chain E residue 640 ILE Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 184 TRP Chi-restraints excluded: chain F residue 304 ASN Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 351 MET Chi-restraints excluded: chain F residue 366 PHE Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 544 ILE Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 435 MET Chi-restraints excluded: chain H residue 214 MET Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 448 VAL Chi-restraints excluded: chain H residue 456 ASP Chi-restraints excluded: chain H residue 492 VAL Chi-restraints excluded: chain H residue 519 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 401 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 237 optimal weight: 0.9980 chunk 303 optimal weight: 0.9980 chunk 235 optimal weight: 0.7980 chunk 350 optimal weight: 2.9990 chunk 232 optimal weight: 0.5980 chunk 414 optimal weight: 10.0000 chunk 259 optimal weight: 0.6980 chunk 252 optimal weight: 0.7980 chunk 191 optimal weight: 2.9990 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 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 243 ASN H 235 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 40382 Z= 0.169 Angle : 0.546 10.825 55877 Z= 0.301 Chirality : 0.039 0.170 6250 Planarity : 0.004 0.059 6036 Dihedral : 22.777 174.494 7704 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.83 % Allowed : 11.99 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 0.37 (0.13), residues: 3985 helix: 1.62 (0.13), residues: 1659 sheet: -0.65 (0.21), residues: 577 loop : -0.75 (0.15), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP B 830 HIS 0.005 0.001 HIS A 69 PHE 0.021 0.001 PHE C 396 TYR 0.017 0.001 TYR G 140 ARG 0.004 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 179 time to evaluate : 4.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 217 TYR cc_start: 0.0954 (OUTLIER) cc_final: 0.0121 (m-80) REVERT: C 229 GLU cc_start: 0.7370 (mm-30) cc_final: 0.6677 (mp0) REVERT: C 287 TYR cc_start: 0.6680 (OUTLIER) cc_final: 0.4955 (m-80) REVERT: C 836 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.7986 (tm130) REVERT: E 321 MET cc_start: 0.6597 (mmp) cc_final: 0.6176 (mtm) REVERT: E 385 SER cc_start: 0.8050 (OUTLIER) cc_final: 0.7692 (m) REVERT: E 567 MET cc_start: 0.8727 (mmm) cc_final: 0.8479 (mmm) REVERT: F 184 TRP cc_start: 0.7352 (OUTLIER) cc_final: 0.6890 (p-90) REVERT: F 469 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7477 (pp) REVERT: H 234 MET cc_start: 0.1756 (mmm) cc_final: 0.0881 (ppp) outliers start: 67 outliers final: 45 residues processed: 239 average time/residue: 0.4572 time to fit residues: 190.7657 Evaluate side-chains 209 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 158 time to evaluate : 4.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 395 TYR Chi-restraints excluded: chain B residue 972 ASN Chi-restraints excluded: chain B residue 1004 ASP Chi-restraints excluded: chain B residue 1101 GLU Chi-restraints excluded: chain C residue 198 PHE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 287 TYR Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 836 GLN Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 308 LYS Chi-restraints excluded: chain E residue 379 HIS Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 467 ILE Chi-restraints excluded: chain E residue 593 SER Chi-restraints excluded: chain E residue 616 ILE Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 184 TRP Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 351 MET Chi-restraints excluded: chain F residue 366 PHE Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 245 GLU Chi-restraints excluded: chain H residue 214 MET Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 448 VAL Chi-restraints excluded: chain H residue 456 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 256 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 chunk 247 optimal weight: 0.0570 chunk 124 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 263 optimal weight: 5.9990 chunk 282 optimal weight: 0.8980 chunk 204 optimal weight: 0.6980 chunk 38 optimal weight: 8.9990 chunk 325 optimal weight: 10.0000 overall best weight: 2.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 40382 Z= 0.268 Angle : 0.586 10.734 55877 Z= 0.318 Chirality : 0.040 0.211 6250 Planarity : 0.004 0.059 6036 Dihedral : 22.776 172.919 7704 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.91 % Allowed : 12.23 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 0.28 (0.13), residues: 3985 helix: 1.55 (0.13), residues: 1659 sheet: -0.66 (0.22), residues: 576 loop : -0.82 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP E 603 HIS 0.006 0.001 HIS D 101 PHE 0.020 0.002 PHE B 368 TYR 0.027 0.002 TYR B 332 ARG 0.004 0.000 ARG F 573 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 162 time to evaluate : 3.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 LYS cc_start: 0.6429 (OUTLIER) cc_final: 0.5761 (tppt) REVERT: C 217 TYR cc_start: 0.1100 (OUTLIER) cc_final: 0.0128 (m-80) REVERT: C 229 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6652 (mp0) REVERT: E 385 SER cc_start: 0.8173 (OUTLIER) cc_final: 0.7811 (m) REVERT: E 567 MET cc_start: 0.8735 (mmm) cc_final: 0.8472 (mmm) REVERT: F 431 MET cc_start: 0.6645 (mtt) cc_final: 0.6144 (mtt) REVERT: F 469 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7707 (pp) REVERT: G 169 HIS cc_start: 0.7056 (OUTLIER) cc_final: 0.5625 (m-70) REVERT: H 205 LEU cc_start: 0.3454 (tp) cc_final: 0.2909 (mm) REVERT: H 234 MET cc_start: 0.1734 (mmm) cc_final: 0.0853 (ppp) outliers start: 70 outliers final: 56 residues processed: 223 average time/residue: 0.4688 time to fit residues: 180.5305 Evaluate side-chains 214 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 153 time to evaluate : 4.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 395 TYR Chi-restraints excluded: chain B residue 763 ASP Chi-restraints excluded: chain B residue 1004 ASP Chi-restraints excluded: chain B residue 1101 GLU Chi-restraints excluded: chain C residue 198 PHE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 308 LYS Chi-restraints excluded: chain E residue 379 HIS Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 467 ILE Chi-restraints excluded: chain E residue 525 SER Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 550 VAL Chi-restraints excluded: chain E residue 593 SER Chi-restraints excluded: chain E residue 616 ILE Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 184 TRP Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 351 MET Chi-restraints excluded: chain F residue 366 PHE Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 520 THR Chi-restraints excluded: chain F residue 544 ILE Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 448 VAL Chi-restraints excluded: chain H residue 456 ASP Chi-restraints excluded: chain H residue 492 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 377 optimal weight: 20.0000 chunk 397 optimal weight: 10.0000 chunk 362 optimal weight: 6.9990 chunk 386 optimal weight: 6.9990 chunk 396 optimal weight: 9.9990 chunk 232 optimal weight: 0.9990 chunk 168 optimal weight: 7.9990 chunk 303 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 349 optimal weight: 0.9990 chunk 365 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN D 99 ASN ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 40382 Z= 0.328 Angle : 0.636 11.335 55877 Z= 0.344 Chirality : 0.042 0.180 6250 Planarity : 0.004 0.066 6036 Dihedral : 22.893 172.974 7704 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.21 % Allowed : 12.26 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 3985 helix: 1.28 (0.13), residues: 1666 sheet: -0.82 (0.21), residues: 576 loop : -1.01 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 830 HIS 0.006 0.001 HIS E 588 PHE 0.022 0.002 PHE C 396 TYR 0.030 0.002 TYR B 332 ARG 0.005 0.001 ARG F 573 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 165 time to evaluate : 4.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 373 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7758 (tm-30) REVERT: C 217 TYR cc_start: 0.1027 (OUTLIER) cc_final: 0.0116 (m-80) REVERT: C 238 MET cc_start: 0.1913 (ttt) cc_final: 0.1668 (ttt) REVERT: C 287 TYR cc_start: 0.6369 (OUTLIER) cc_final: 0.4744 (m-80) REVERT: C 558 MET cc_start: 0.1034 (tpp) cc_final: 0.0808 (tpt) REVERT: C 566 ARG cc_start: 0.3222 (tpt170) cc_final: 0.2440 (ttt180) REVERT: E 385 SER cc_start: 0.8343 (OUTLIER) cc_final: 0.7938 (m) REVERT: F 207 MET cc_start: 0.7639 (mpp) cc_final: 0.6437 (mtp) REVERT: F 431 MET cc_start: 0.6756 (mtt) cc_final: 0.6456 (mtt) REVERT: F 469 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7828 (pp) REVERT: G 169 HIS cc_start: 0.7249 (OUTLIER) cc_final: 0.5555 (m-70) REVERT: H 205 LEU cc_start: 0.3244 (tp) cc_final: 0.2809 (mm) REVERT: H 234 MET cc_start: 0.1710 (mmm) cc_final: 0.0782 (ppp) outliers start: 81 outliers final: 66 residues processed: 234 average time/residue: 0.4837 time to fit residues: 193.6055 Evaluate side-chains 225 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 154 time to evaluate : 4.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 395 TYR Chi-restraints excluded: chain B residue 763 ASP Chi-restraints excluded: chain B residue 1004 ASP Chi-restraints excluded: chain B residue 1101 GLU Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 198 PHE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 287 TYR Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 308 LYS Chi-restraints excluded: chain E residue 379 HIS Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 467 ILE Chi-restraints excluded: chain E residue 525 SER Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 550 VAL Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 593 SER Chi-restraints excluded: chain E residue 616 ILE Chi-restraints excluded: chain E residue 643 THR Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 184 TRP Chi-restraints excluded: chain F residue 304 ASN Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 351 MET Chi-restraints excluded: chain F residue 366 PHE Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 544 ILE Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 448 VAL Chi-restraints excluded: chain H residue 456 ASP Chi-restraints excluded: chain H residue 492 VAL Chi-restraints excluded: chain H residue 523 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 384 optimal weight: 0.8980 chunk 253 optimal weight: 1.9990 chunk 408 optimal weight: 10.0000 chunk 249 optimal weight: 2.9990 chunk 193 optimal weight: 0.8980 chunk 283 optimal weight: 0.4980 chunk 428 optimal weight: 20.0000 chunk 394 optimal weight: 7.9990 chunk 341 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 263 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 HIS ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 40382 Z= 0.175 Angle : 0.557 12.251 55877 Z= 0.303 Chirality : 0.039 0.169 6250 Planarity : 0.004 0.069 6036 Dihedral : 22.763 172.676 7704 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.50 % Allowed : 13.11 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 0.30 (0.13), residues: 3985 helix: 1.60 (0.13), residues: 1664 sheet: -0.70 (0.21), residues: 578 loop : -0.84 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP B 830 HIS 0.005 0.001 HIS G 169 PHE 0.025 0.001 PHE B 466 TYR 0.023 0.001 TYR B 332 ARG 0.007 0.000 ARG H 431 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 177 time to evaluate : 4.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 373 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7734 (tm-30) REVERT: C 217 TYR cc_start: 0.1046 (OUTLIER) cc_final: 0.0192 (m-80) REVERT: C 229 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6249 (mp0) REVERT: C 287 TYR cc_start: 0.6547 (OUTLIER) cc_final: 0.4839 (m-80) REVERT: C 566 ARG cc_start: 0.3260 (tpt170) cc_final: 0.2571 (ttt180) REVERT: C 1019 MET cc_start: 0.8637 (ttm) cc_final: 0.8181 (tpp) REVERT: D 192 LYS cc_start: 0.8111 (mttp) cc_final: 0.7697 (mtmm) REVERT: E 385 SER cc_start: 0.8127 (OUTLIER) cc_final: 0.7747 (m) REVERT: F 184 TRP cc_start: 0.7434 (OUTLIER) cc_final: 0.7004 (p-90) REVERT: F 469 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7826 (pp) REVERT: H 234 MET cc_start: 0.1651 (mmm) cc_final: 0.0916 (ppp) outliers start: 55 outliers final: 47 residues processed: 224 average time/residue: 0.5122 time to fit residues: 199.4740 Evaluate side-chains 212 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 160 time to evaluate : 4.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 395 TYR Chi-restraints excluded: chain B residue 763 ASP Chi-restraints excluded: chain B residue 1004 ASP Chi-restraints excluded: chain B residue 1101 GLU Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 198 PHE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 287 TYR Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain D residue 636 MET Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 308 LYS Chi-restraints excluded: chain E residue 379 HIS Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 467 ILE Chi-restraints excluded: chain E residue 525 SER Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 593 SER Chi-restraints excluded: chain E residue 616 ILE Chi-restraints excluded: chain E residue 643 THR Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 184 TRP Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 351 MET Chi-restraints excluded: chain F residue 366 PHE Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 448 VAL Chi-restraints excluded: chain H residue 456 ASP Chi-restraints excluded: chain H residue 523 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 209 optimal weight: 0.7980 chunk 270 optimal weight: 0.9990 chunk 363 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 314 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 94 optimal weight: 8.9990 chunk 341 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 350 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 HIS ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.149570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.127457 restraints weight = 112908.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.128862 restraints weight = 252990.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.128827 restraints weight = 102372.652| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 40382 Z= 0.193 Angle : 0.558 13.920 55877 Z= 0.301 Chirality : 0.039 0.165 6250 Planarity : 0.004 0.064 6036 Dihedral : 22.721 171.527 7704 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.53 % Allowed : 13.13 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 3985 helix: 1.65 (0.13), residues: 1668 sheet: -0.66 (0.22), residues: 558 loop : -0.84 (0.15), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP B 830 HIS 0.005 0.001 HIS G 169 PHE 0.025 0.001 PHE C 396 TYR 0.023 0.001 TYR B 332 ARG 0.007 0.000 ARG H 416 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6302.76 seconds wall clock time: 117 minutes 38.71 seconds (7058.71 seconds total)