Starting phenix.real_space_refine on Tue Apr 16 19:08:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3i_15829/04_2024/8b3i_15829.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3i_15829/04_2024/8b3i_15829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3i_15829/04_2024/8b3i_15829.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3i_15829/04_2024/8b3i_15829.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3i_15829/04_2024/8b3i_15829.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3i_15829/04_2024/8b3i_15829.pdb" } resolution = 3.5 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= 0.137 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 3 6.06 5 S 118 5.16 5 C 12801 2.51 5 N 3480 2.21 5 O 3795 1.98 5 H 20180 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 122": "OE1" <-> "OE2" Residue "N GLU 18": "OE1" <-> "OE2" Residue "N GLU 32": "OE1" <-> "OE2" Residue "R GLU 55": "OE1" <-> "OE2" Residue "R GLU 67": "OE1" <-> "OE2" Residue "U GLU 16": "OE1" <-> "OE2" Residue "U GLU 18": "OE1" <-> "OE2" Residue "U ASP 39": "OD1" <-> "OD2" Residue "U TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 55": "OE1" <-> "OE2" Residue "a GLU 74": "OE1" <-> "OE2" Residue "a GLU 188": "OE1" <-> "OE2" Residue "a GLU 238": "OE1" <-> "OE2" Residue "d GLU 65": "OE1" <-> "OE2" Residue "d GLU 72": "OE1" <-> "OE2" Residue "d PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d GLU 224": "OE1" <-> "OE2" Residue "d TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d GLU 303": "OE1" <-> "OE2" Residue "d GLU 398": "OE1" <-> "OE2" Residue "d GLU 441": "OE1" <-> "OE2" Residue "d GLU 444": "OE1" <-> "OE2" Residue "d GLU 489": "OE1" <-> "OE2" Residue "d GLU 492": "OE1" <-> "OE2" Residue "d GLU 525": "OE1" <-> "OE2" Residue "d GLU 537": "OE1" <-> "OE2" Residue "d GLU 575": "OE1" <-> "OE2" Residue "d GLU 580": "OE1" <-> "OE2" Residue "d GLU 585": "OE1" <-> "OE2" Residue "d GLU 597": "OE1" <-> "OE2" Residue "d PHE 650": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d GLU 706": "OE1" <-> "OE2" Residue "d GLU 842": "OE1" <-> "OE2" Residue "d GLU 896": "OE1" <-> "OE2" Residue "d GLU 898": "OE1" <-> "OE2" Residue "d GLU 969": "OE1" <-> "OE2" Residue "d GLU 1045": "OE1" <-> "OE2" Residue "d GLU 1135": "OE1" <-> "OE2" Residue "e PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e ARG 51": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "e TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e GLU 68": "OE1" <-> "OE2" Residue "e GLU 84": "OE1" <-> "OE2" Residue "e GLU 111": "OE1" <-> "OE2" Residue "e GLU 123": "OE1" <-> "OE2" Residue "e PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e GLU 201": "OE1" <-> "OE2" Residue "e GLU 203": "OE1" <-> "OE2" Residue "e TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e GLU 232": "OE1" <-> "OE2" Residue "e GLU 238": "OE1" <-> "OE2" Residue "e GLU 246": "OE1" <-> "OE2" Residue "e GLU 253": "OE1" <-> "OE2" Residue "e GLU 255": "OE1" <-> "OE2" Residue "e GLU 269": "OE1" <-> "OE2" Residue "e GLU 270": "OE1" <-> "OE2" Residue "e GLU 297": "OE1" <-> "OE2" Residue "e GLU 313": "OE1" <-> "OE2" Residue "e GLU 377": "OE1" <-> "OE2" Residue "e GLU 384": "OE1" <-> "OE2" Residue "e GLU 392": "OE1" <-> "OE2" Residue "e GLU 395": "OE1" <-> "OE2" Residue "e GLU 407": "OE1" <-> "OE2" Residue "e GLU 423": "OE1" <-> "OE2" Residue "e GLU 428": "OE1" <-> "OE2" Residue "e GLU 450": "OE1" <-> "OE2" Residue "e GLU 472": "OE1" <-> "OE2" Residue "e GLU 492": "OE1" <-> "OE2" Residue "e GLU 499": "OE1" <-> "OE2" Residue "e GLU 540": "OE1" <-> "OE2" Residue "e GLU 546": "OE1" <-> "OE2" Residue "e GLU 581": "OE1" <-> "OE2" Residue "e GLU 584": "OE1" <-> "OE2" Residue "e GLU 588": "OE1" <-> "OE2" Residue "e PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e GLU 604": "OE1" <-> "OE2" Residue "e GLU 611": "OE1" <-> "OE2" Residue "e GLU 612": "OE1" <-> "OE2" Residue "e GLU 647": "OE1" <-> "OE2" Residue "e GLU 649": "OE1" <-> "OE2" Residue "e PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e GLU 659": "OE1" <-> "OE2" Residue "e GLU 718": "OE1" <-> "OE2" Residue "e GLU 737": "OE1" <-> "OE2" Residue "e GLU 746": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 40377 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 2290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2290 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 15, 'TRANS': 130} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 1237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1237 Classifications: {'peptide': 76} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "R" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1284 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain breaks: 1 Chain: "U" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1207 Classifications: {'peptide': 76} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "a" Number of atoms: 5627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 5627 Classifications: {'peptide': 365} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 355} Chain: "d" Number of atoms: 17196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1096, 17196 Classifications: {'peptide': 1096} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 1055} Chain breaks: 6 Chain: "e" Number of atoms: 11533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 11533 Classifications: {'peptide': 699} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 679} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3935 SG CYS R 42 65.760 82.049 142.272 1.00 51.27 S ATOM 3974 SG CYS R 45 67.643 80.995 140.268 1.00 47.50 S ATOM 4437 SG CYS R 83 68.813 84.450 140.531 1.00 53.62 S ATOM 4312 SG CYS R 75 57.082 89.042 151.310 1.00 64.78 S ATOM 4637 SG CYS R 94 58.570 88.624 147.211 1.00 58.83 S ATOM 4106 SG CYS R 53 72.027 83.527 139.811 1.00 64.90 S ATOM 4150 SG CYS R 56 75.951 83.499 140.927 1.00 66.80 S ATOM 4215 SG CYS R 68 74.085 82.511 143.351 1.00 65.16 S Time building chain proxies: 17.48, per 1000 atoms: 0.43 Number of scatterers: 40377 At special positions: 0 Unit cell: (103.95, 139.65, 187.95, 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 3 29.99 S 118 16.00 O 3795 8.00 N 3480 7.00 C 12801 6.00 H 20180 1.00 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: 33.24 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 45 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" ND1 HIS R 77 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 75 " pdb=" ZN R 203 " pdb="ZN ZN R 203 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 56 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 68 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 53 " Number of angles added : 6 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4760 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 44 sheets defined 28.8% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.76 Creating SS restraints... Processing helix chain 'D' and resid 2 through 16 removed outlier: 3.660A pdb=" N ILE D 6 " --> pdb=" O ALA D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 63 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 98 through 110 removed outlier: 3.515A pdb=" N LEU D 104 " --> pdb=" O SER D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 130 removed outlier: 3.839A pdb=" N ILE D 126 " --> pdb=" O GLU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 146 removed outlier: 3.612A pdb=" N TYR D 134 " --> pdb=" O ASP D 130 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG D 136 " --> pdb=" O GLU D 132 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG D 139 " --> pdb=" O ASN D 135 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 35 removed outlier: 3.522A pdb=" N ILE N 26 " --> pdb=" O LYS N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 39 No H-bonds generated for 'chain 'N' and resid 37 through 39' Processing helix chain 'N' and resid 55 through 60 Processing helix chain 'R' and resid 53 through 58 removed outlier: 4.205A pdb=" N ALA R 58 " --> pdb=" O ILE R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 91 removed outlier: 4.050A pdb=" N ARG R 86 " --> pdb=" O HIS R 82 " (cutoff:3.500A) Processing helix chain 'U' and resid 22 through 35 Processing helix chain 'U' and resid 55 through 60 removed outlier: 3.528A pdb=" N ASN U 60 " --> pdb=" O SER U 57 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 10 Processing helix chain 'a' and resid 14 through 29 removed outlier: 3.918A pdb=" N LEU a 18 " --> pdb=" O ASP a 14 " (cutoff:3.500A) Processing helix chain 'd' and resid 251 through 255 Processing helix chain 'd' and resid 366 through 370 removed outlier: 4.121A pdb=" N GLN d 370 " --> pdb=" O LEU d 367 " (cutoff:3.500A) Processing helix chain 'd' and resid 755 through 759 Processing helix chain 'd' and resid 986 through 990 Processing helix chain 'd' and resid 1044 through 1062 Processing helix chain 'd' and resid 1069 through 1074 Processing helix chain 'd' and resid 1091 through 1096 Processing helix chain 'd' and resid 1101 through 1109 Processing helix chain 'd' and resid 1125 through 1138 Processing helix chain 'e' and resid 57 through 75 Processing helix chain 'e' and resid 82 through 96 Processing helix chain 'e' and resid 98 through 122 removed outlier: 3.506A pdb=" N ALA e 109 " --> pdb=" O GLN e 105 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN e 115 " --> pdb=" O GLU e 111 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA e 116 " --> pdb=" O ASP e 112 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU e 119 " --> pdb=" O GLN e 115 " (cutoff:3.500A) Proline residue: e 120 - end of helix Processing helix chain 'e' and resid 127 through 153 removed outlier: 3.585A pdb=" N LYS e 133 " --> pdb=" O VAL e 129 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS e 142 " --> pdb=" O CYS e 138 " (cutoff:3.500A) Processing helix chain 'e' and resid 153 through 159 Processing helix chain 'e' and resid 159 through 164 removed outlier: 3.947A pdb=" N GLN e 163 " --> pdb=" O THR e 159 " (cutoff:3.500A) Processing helix chain 'e' and resid 169 through 182 Processing helix chain 'e' and resid 185 through 205 Processing helix chain 'e' and resid 210 through 224 Processing helix chain 'e' and resid 226 through 252 removed outlier: 3.580A pdb=" N GLU e 232 " --> pdb=" O LYS e 228 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU e 233 " --> pdb=" O ASP e 229 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS e 234 " --> pdb=" O SER e 230 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN e 252 " --> pdb=" O GLN e 248 " (cutoff:3.500A) Processing helix chain 'e' and resid 255 through 277 removed outlier: 3.648A pdb=" N ASN e 261 " --> pdb=" O PRO e 257 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE e 275 " --> pdb=" O GLY e 271 " (cutoff:3.500A) Processing helix chain 'e' and resid 279 through 281 No H-bonds generated for 'chain 'e' and resid 279 through 281' Processing helix chain 'e' and resid 282 through 295 Processing helix chain 'e' and resid 298 through 314 removed outlier: 4.670A pdb=" N ASP e 308 " --> pdb=" O GLN e 304 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N HIS e 309 " --> pdb=" O LYS e 305 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP e 312 " --> pdb=" O ASP e 308 " (cutoff:3.500A) Processing helix chain 'e' and resid 315 through 327 Processing helix chain 'e' and resid 331 through 353 removed outlier: 3.599A pdb=" N HIS e 339 " --> pdb=" O ALA e 335 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR e 349 " --> pdb=" O LYS e 345 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA e 350 " --> pdb=" O THR e 346 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE e 351 " --> pdb=" O PHE e 347 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL e 352 " --> pdb=" O GLY e 348 " (cutoff:3.500A) Processing helix chain 'e' and resid 354 through 358 Processing helix chain 'e' and resid 361 through 379 Processing helix chain 'e' and resid 383 through 399 removed outlier: 3.883A pdb=" N ASN e 399 " --> pdb=" O GLU e 395 " (cutoff:3.500A) Processing helix chain 'e' and resid 403 through 418 removed outlier: 3.629A pdb=" N GLU e 407 " --> pdb=" O ASN e 403 " (cutoff:3.500A) Processing helix chain 'e' and resid 425 through 441 removed outlier: 3.605A pdb=" N ARG e 431 " --> pdb=" O GLU e 427 " (cutoff:3.500A) Processing helix chain 'e' and resid 445 through 463 removed outlier: 3.537A pdb=" N PHE e 449 " --> pdb=" O GLY e 445 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA e 451 " --> pdb=" O ASP e 447 " (cutoff:3.500A) Processing helix chain 'e' and resid 468 through 488 removed outlier: 7.631A pdb=" N ALA e 485 " --> pdb=" O HIS e 481 " (cutoff:3.500A) removed outlier: 9.445A pdb=" N ALA e 486 " --> pdb=" O GLU e 482 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE e 487 " --> pdb=" O CYS e 483 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR e 488 " --> pdb=" O GLY e 484 " (cutoff:3.500A) Processing helix chain 'e' and resid 488 through 515 removed outlier: 3.577A pdb=" N MET e 494 " --> pdb=" O LYS e 490 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE e 495 " --> pdb=" O LEU e 491 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP e 503 " --> pdb=" O GLU e 499 " (cutoff:3.500A) Processing helix chain 'e' and resid 544 through 562 removed outlier: 3.675A pdb=" N LYS e 549 " --> pdb=" O PRO e 545 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU e 550 " --> pdb=" O GLU e 546 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN e 551 " --> pdb=" O MET e 547 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU e 552 " --> pdb=" O ILE e 548 " (cutoff:3.500A) Processing helix chain 'e' and resid 593 through 600 Processing helix chain 'e' and resid 610 through 618 removed outlier: 3.793A pdb=" N ALA e 616 " --> pdb=" O GLU e 612 " (cutoff:3.500A) Processing helix chain 'e' and resid 620 through 633 Processing helix chain 'e' and resid 693 through 708 Processing helix chain 'e' and resid 712 through 723 removed outlier: 3.581A pdb=" N LEU e 719 " --> pdb=" O LEU e 715 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR e 720 " --> pdb=" O VAL e 716 " (cutoff:3.500A) Processing helix chain 'e' and resid 728 through 742 Processing sheet with id=AA1, first strand: chain 'D' and resid 21 through 25 Processing sheet with id=AA2, first strand: chain 'N' and resid 12 through 16 removed outlier: 7.824A pdb=" N LEU N 67 " --> pdb=" O LEU N 2 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS N 4 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU N 69 " --> pdb=" O LYS N 4 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS N 6 " --> pdb=" O LEU N 69 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N LEU N 71 " --> pdb=" O LYS N 6 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL N 70 " --> pdb=" O ARG N 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'e' and resid 522 through 529 removed outlier: 3.814A pdb=" N VAL e 577 " --> pdb=" O LYS R 26 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N VAL R 30 " --> pdb=" O LEU e 573 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU e 573 " --> pdb=" O VAL R 30 " (cutoff:3.500A) removed outlier: 11.183A pdb=" N LEU R 32 " --> pdb=" O THR e 571 " (cutoff:3.500A) removed outlier: 10.139A pdb=" N THR e 571 " --> pdb=" O LEU R 32 " (cutoff:3.500A) removed outlier: 10.644A pdb=" N ALA R 34 " --> pdb=" O TRP e 569 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N TRP e 569 " --> pdb=" O ALA R 34 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY e 585 " --> pdb=" O PHE e 582 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE e 582 " --> pdb=" O GLY e 585 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'e' and resid 522 through 529 removed outlier: 3.814A pdb=" N VAL e 577 " --> pdb=" O LYS R 26 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N VAL R 30 " --> pdb=" O LEU e 573 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU e 573 " --> pdb=" O VAL R 30 " (cutoff:3.500A) removed outlier: 11.183A pdb=" N LEU R 32 " --> pdb=" O THR e 571 " (cutoff:3.500A) removed outlier: 10.139A pdb=" N THR e 571 " --> pdb=" O LEU R 32 " (cutoff:3.500A) removed outlier: 10.644A pdb=" N ALA R 34 " --> pdb=" O TRP e 569 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N TRP e 569 " --> pdb=" O ALA R 34 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N ILE e 667 " --> pdb=" O LYS e 586 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N GLU e 588 " --> pdb=" O ILE e 667 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 70 through 72 Processing sheet with id=AA6, first strand: chain 'U' and resid 13 through 16 Processing sheet with id=AA7, first strand: chain 'a' and resid 30 through 32 removed outlier: 3.501A pdb=" N LEU a 359 " --> pdb=" O SER a 351 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'a' and resid 37 through 38 removed outlier: 7.387A pdb=" N ASP a 37 " --> pdb=" O CYS a 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'a' and resid 46 through 51 removed outlier: 6.405A pdb=" N GLY a 62 " --> pdb=" O ASN a 47 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LEU a 49 " --> pdb=" O LEU a 60 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU a 60 " --> pdb=" O LEU a 49 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ILE a 51 " --> pdb=" O TYR a 58 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N TYR a 58 " --> pdb=" O ILE a 51 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET a 59 " --> pdb=" O TYR a 71 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE a 68 " --> pdb=" O ILE a 90 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS a 88 " --> pdb=" O LEU a 70 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'a' and resid 102 through 107 removed outlier: 3.762A pdb=" N THR a 104 " --> pdb=" O SER a 118 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR a 123 " --> pdb=" O SER a 119 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU a 124 " --> pdb=" O VAL a 137 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL a 137 " --> pdb=" O LEU a 124 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL a 126 " --> pdb=" O ALA a 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'a' and resid 144 through 149 removed outlier: 3.707A pdb=" N SER a 146 " --> pdb=" O GLY a 162 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 191 through 194 removed outlier: 3.545A pdb=" N ILE a 224 " --> pdb=" O LEU a 213 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'a' and resid 248 through 253 removed outlier: 3.985A pdb=" N ARG a 268 " --> pdb=" O GLY a 264 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'a' and resid 298 through 299 removed outlier: 3.560A pdb=" N THR a 298 " --> pdb=" O PHE a 309 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE a 316 " --> pdb=" O MET a 329 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N MET a 329 " --> pdb=" O ILE a 316 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL a 318 " --> pdb=" O ILE a 327 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'd' and resid 1007 through 1009 removed outlier: 3.510A pdb=" N PHE d1030 " --> pdb=" O GLY d1038 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE d1037 " --> pdb=" O ALA d 9 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'd' and resid 15 through 21 removed outlier: 3.891A pdb=" N GLY d 17 " --> pdb=" O ALA d 34 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'd' and resid 38 through 41 removed outlier: 4.032A pdb=" N LYS d 53 " --> pdb=" O ILE d 41 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'd' and resid 61 through 67 removed outlier: 6.620A pdb=" N LEU d 80 " --> pdb=" O ALA d 62 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N MET d 64 " --> pdb=" O PHE d 78 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N PHE d 78 " --> pdb=" O MET d 64 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LEU d 66 " --> pdb=" O LEU d 76 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU d 76 " --> pdb=" O LEU d 66 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN d 85 " --> pdb=" O THR d 81 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA d 104 " --> pdb=" O ILE d 88 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLU d 90 " --> pdb=" O THR d 102 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N THR d 102 " --> pdb=" O GLU d 90 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LYS d 92 " --> pdb=" O ILE d 100 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE d 100 " --> pdb=" O LYS d 92 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER d 94 " --> pdb=" O ILE d 98 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE d 98 " --> pdb=" O SER d 94 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'd' and resid 121 through 124 removed outlier: 3.740A pdb=" N ILE d 121 " --> pdb=" O ARG d 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'd' and resid 164 through 169 removed outlier: 6.580A pdb=" N VAL d 181 " --> pdb=" O ILE d 165 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N VAL d 167 " --> pdb=" O CYS d 179 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N CYS d 179 " --> pdb=" O VAL d 167 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N PHE d 169 " --> pdb=" O THR d 177 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR d 177 " --> pdb=" O PHE d 169 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'd' and resid 220 through 221 removed outlier: 3.572A pdb=" N ILE d 248 " --> pdb=" O ILE d 237 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'd' and resid 258 through 263 removed outlier: 3.580A pdb=" N LEU d 273 " --> pdb=" O PHE d 281 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ARG d 279 " --> pdb=" O ASP d 275 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU d 280 " --> pdb=" O LEU d 304 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU d 304 " --> pdb=" O LEU d 280 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N MET d 282 " --> pdb=" O VAL d 302 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL d 302 " --> pdb=" O MET d 282 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU d 284 " --> pdb=" O LEU d 300 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU d 300 " --> pdb=" O LEU d 284 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLU d 286 " --> pdb=" O LYS d 298 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'd' and resid 313 through 318 removed outlier: 4.927A pdb=" N LEU d 314 " --> pdb=" O GLY d 325 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLY d 325 " --> pdb=" O LEU d 314 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N TYR d 316 " --> pdb=" O PHE d 323 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N PHE d 323 " --> pdb=" O TYR d 316 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP d 318 " --> pdb=" O VAL d 321 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER d 331 " --> pdb=" O THR d 352 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N THR d 352 " --> pdb=" O SER d 331 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU d 333 " --> pdb=" O MET d 350 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'd' and resid 362 through 365 Processing sheet with id=AC7, first strand: chain 'd' and resid 386 through 387 Processing sheet with id=AC8, first strand: chain 'd' and resid 390 through 391 Processing sheet with id=AC9, first strand: chain 'd' and resid 396 through 403 removed outlier: 5.707A pdb=" N GLU d 398 " --> pdb=" O THR d 703 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N THR d 703 " --> pdb=" O GLU d 398 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'd' and resid 407 through 413 removed outlier: 4.443A pdb=" N VAL d 435 " --> pdb=" O THR d 446 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'd' and resid 470 through 471 removed outlier: 3.506A pdb=" N SER d 488 " --> pdb=" O LEU d 478 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N SER d 480 " --> pdb=" O LEU d 486 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU d 486 " --> pdb=" O SER d 480 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'd' and resid 500 through 503 removed outlier: 6.614A pdb=" N LEU d 516 " --> pdb=" O HIS d 531 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N HIS d 531 " --> pdb=" O LEU d 516 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N TYR d 518 " --> pdb=" O ILE d 529 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'd' and resid 538 through 542 removed outlier: 6.520A pdb=" N GLY d 559 " --> pdb=" O ALA d 539 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU d 541 " --> pdb=" O ALA d 557 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ALA d 557 " --> pdb=" O LEU d 541 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER d 565 " --> pdb=" O LEU d 560 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS d 578 " --> pdb=" O ILE d 568 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS d 570 " --> pdb=" O LEU d 576 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LEU d 576 " --> pdb=" O LYS d 570 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'd' and resid 588 through 596 removed outlier: 3.521A pdb=" N SER d 590 " --> pdb=" O ALA d 605 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE d 614 " --> pdb=" O LEU d 602 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA d 610 " --> pdb=" O LEU d 606 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU d 611 " --> pdb=" O LYS d 628 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LYS d 628 " --> pdb=" O LEU d 611 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TYR d 613 " --> pdb=" O ARG d 626 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ARG d 626 " --> pdb=" O TYR d 613 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'd' and resid 637 through 642 removed outlier: 8.466A pdb=" N THR d 647 " --> pdb=" O SER d 661 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N SER d 661 " --> pdb=" O THR d 647 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'd' and resid 681 through 682 Processing sheet with id=AD8, first strand: chain 'd' and resid 720 through 727 removed outlier: 6.176A pdb=" N SER d 738 " --> pdb=" O PRO d 721 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS d 723 " --> pdb=" O LEU d 736 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS d 732 " --> pdb=" O GLN d 727 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER d 737 " --> pdb=" O ASN d 790 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG d 739 " --> pdb=" O VAL d 788 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N HIS d 789 " --> pdb=" O GLN d 806 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLN d 806 " --> pdb=" O HIS d 789 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU d 791 " --> pdb=" O ALA d 804 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ALA d 804 " --> pdb=" O LEU d 791 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE d 793 " --> pdb=" O LEU d 802 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER d 762 " --> pdb=" O ALA d 804 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N GLN d 806 " --> pdb=" O SER d 762 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N SER d 764 " --> pdb=" O GLN d 806 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'd' and resid 811 through 819 removed outlier: 5.468A pdb=" N ALA d 813 " --> pdb=" O ALA d 834 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA d 834 " --> pdb=" O ALA d 813 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG d 847 " --> pdb=" O THR d 833 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL d 850 " --> pdb=" O VAL d 861 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'd' and resid 811 through 819 removed outlier: 5.468A pdb=" N ALA d 813 " --> pdb=" O ALA d 834 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA d 834 " --> pdb=" O ALA d 813 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG d 847 " --> pdb=" O THR d 833 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY d 846 " --> pdb=" O VAL d 866 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'd' and resid 874 through 876 Processing sheet with id=AE3, first strand: chain 'd' and resid 890 through 893 removed outlier: 6.792A pdb=" N LEU d 890 " --> pdb=" O GLU d 902 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'd' and resid 911 through 917 removed outlier: 3.731A pdb=" N ASN d 941 " --> pdb=" O LYS d 936 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'd' and resid 954 through 961 removed outlier: 6.489A pdb=" N ASN d 964 " --> pdb=" O LEU d 960 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU d 974 " --> pdb=" O LEU d 997 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU d 997 " --> pdb=" O LEU d 974 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL d 976 " --> pdb=" O VAL d 995 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'd' and resid 1076 through 1078 Processing sheet with id=AE7, first strand: chain 'e' and resid 607 through 609 removed outlier: 3.502A pdb=" N PHE e 654 " --> pdb=" O PHE e 608 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'e' and resid 709 through 711 815 hydrogen bonds defined for protein. 2274 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.05 Time building geometry restraints manager: 34.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 20135 1.03 - 1.23: 81 1.23 - 1.42: 8461 1.42 - 1.62: 11903 1.62 - 1.82: 180 Bond restraints: 40760 Sorted by residual: bond pdb=" CB PRO e 520 " pdb=" CG PRO e 520 " ideal model delta sigma weight residual 1.492 1.583 -0.091 5.00e-02 4.00e+02 3.33e+00 bond pdb=" C GLU d 40 " pdb=" N ILE d 41 " ideal model delta sigma weight residual 1.334 1.313 0.021 1.29e-02 6.01e+03 2.60e+00 bond pdb=" CD2 TYR a 145 " pdb=" CE2 TYR a 145 " ideal model delta sigma weight residual 1.382 1.337 0.045 3.00e-02 1.11e+03 2.23e+00 bond pdb=" CB TYR a 145 " pdb=" CG TYR a 145 " ideal model delta sigma weight residual 1.512 1.482 0.030 2.20e-02 2.07e+03 1.86e+00 bond pdb=" CB MET d 954 " pdb=" CG MET d 954 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.78e+00 ... (remaining 40755 not shown) Histogram of bond angle deviations from ideal: 97.64 - 104.93: 292 104.93 - 112.21: 47368 112.21 - 119.49: 9981 119.49 - 126.78: 15848 126.78 - 134.06: 253 Bond angle restraints: 73742 Sorted by residual: angle pdb=" CA PRO e 520 " pdb=" N PRO e 520 " pdb=" CD PRO e 520 " ideal model delta sigma weight residual 112.00 103.95 8.05 1.40e+00 5.10e-01 3.30e+01 angle pdb=" N SER d 929 " pdb=" CA SER d 929 " pdb=" C SER d 929 " ideal model delta sigma weight residual 110.80 119.33 -8.53 2.13e+00 2.20e-01 1.60e+01 angle pdb=" N ILE d 884 " pdb=" CA ILE d 884 " pdb=" C ILE d 884 " ideal model delta sigma weight residual 110.05 106.19 3.86 1.09e+00 8.42e-01 1.25e+01 angle pdb=" N ARG R 91 " pdb=" CA ARG R 91 " pdb=" C ARG R 91 " ideal model delta sigma weight residual 107.93 112.89 -4.96 1.65e+00 3.67e-01 9.05e+00 angle pdb=" N VAL a 237 " pdb=" CA VAL a 237 " pdb=" C VAL a 237 " ideal model delta sigma weight residual 106.21 109.40 -3.19 1.07e+00 8.73e-01 8.87e+00 ... (remaining 73737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 17018 17.59 - 35.18: 1591 35.18 - 52.77: 329 52.77 - 70.36: 88 70.36 - 87.94: 18 Dihedral angle restraints: 19044 sinusoidal: 10467 harmonic: 8577 Sorted by residual: dihedral pdb=" CA ILE d 884 " pdb=" C ILE d 884 " pdb=" N ASN d 885 " pdb=" CA ASN d 885 " ideal model delta harmonic sigma weight residual -180.00 -151.06 -28.94 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA ASN e 57 " pdb=" C ASN e 57 " pdb=" N TYR e 58 " pdb=" CA TYR e 58 " ideal model delta harmonic sigma weight residual -180.00 -154.87 -25.13 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA ARG e 51 " pdb=" C ARG e 51 " pdb=" N PRO e 52 " pdb=" CA PRO e 52 " ideal model delta harmonic sigma weight residual 180.00 -155.41 -24.59 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 19041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1993 0.034 - 0.068: 778 0.068 - 0.102: 227 0.102 - 0.136: 128 0.136 - 0.170: 8 Chirality restraints: 3134 Sorted by residual: chirality pdb=" CB VAL d 930 " pdb=" CA VAL d 930 " pdb=" CG1 VAL d 930 " pdb=" CG2 VAL d 930 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.26e-01 chirality pdb=" CA SER d 929 " pdb=" N SER d 929 " pdb=" C SER d 929 " pdb=" CB SER d 929 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CG LEU d1129 " pdb=" CB LEU d1129 " pdb=" CD1 LEU d1129 " pdb=" CD2 LEU d1129 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.76e-01 ... (remaining 3131 not shown) Planarity restraints: 6003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY e 519 " 0.090 5.00e-02 4.00e+02 1.32e-01 2.77e+01 pdb=" N PRO e 520 " -0.227 5.00e-02 4.00e+02 pdb=" CA PRO e 520 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO e 520 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP a 272 " -0.012 2.00e-02 2.50e+03 1.46e-02 8.55e+00 pdb=" CG TRP a 272 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP a 272 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP a 272 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP a 272 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP a 272 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP a 272 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 272 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 272 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP a 272 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP a 272 " -0.010 2.00e-02 2.50e+03 pdb=" HE1 TRP a 272 " 0.004 2.00e-02 2.50e+03 pdb=" HE3 TRP a 272 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP a 272 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP a 272 " 0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP a 272 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER d 929 " -0.011 2.00e-02 2.50e+03 2.30e-02 5.30e+00 pdb=" C SER d 929 " 0.040 2.00e-02 2.50e+03 pdb=" O SER d 929 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL d 930 " -0.014 2.00e-02 2.50e+03 ... (remaining 6000 not shown) Histogram of nonbonded interaction distances: 1.27 - 1.94: 229 1.94 - 2.60: 47794 2.60 - 3.27: 123451 3.27 - 3.93: 158732 3.93 - 4.60: 251484 Nonbonded interactions: 581690 Sorted by model distance: nonbonded pdb=" SG CYS R 75 " pdb=" OD2 ASP R 97 " model vdw 1.270 3.200 nonbonded pdb="HG23 ILE D 37 " pdb=" SG CYS D 107 " model vdw 1.535 3.020 nonbonded pdb=" OE2 GLU d 537 " pdb=" H GLU e 84 " model vdw 1.611 1.850 nonbonded pdb=" H ASP R 36 " pdb=" O GLY e 564 " model vdw 1.622 1.850 nonbonded pdb=" H ALA d 869 " pdb=" OD1 ASN d 885 " model vdw 1.625 1.850 ... (remaining 581685 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.580 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: 0.650 Extract box with map and model: 10.730 Check model and map are aligned: 0.580 Set scattering table: 0.290 Process input model: 145.080 Find NCS groups from input model: 0.780 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 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 : 0.005 0.091 20580 Z= 0.338 Angle : 0.636 8.533 27806 Z= 0.343 Chirality : 0.044 0.170 3134 Planarity : 0.004 0.132 3570 Dihedral : 13.764 87.945 7706 Min Nonbonded Distance : 1.270 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: -2.21 (0.16), residues: 2507 helix: 0.09 (0.21), residues: 646 sheet: -2.42 (0.19), residues: 665 loop : -1.68 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP a 272 HIS 0.009 0.001 HIS R 48 PHE 0.032 0.002 PHE e 48 TYR 0.018 0.001 TYR a 145 ARG 0.004 0.000 ARG e 702 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 2255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 3.685 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 outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.7435 time to fit residues: 207.8286 Evaluate side-chains 128 residues out of total 2255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 3.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 210 optimal weight: 2.9990 chunk 188 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 226 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 189 HIS ** d 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 145 GLN e 164 ASN e 309 HIS e 338 GLN e 722 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 20580 Z= 0.389 Angle : 0.614 8.435 27806 Z= 0.334 Chirality : 0.044 0.169 3134 Planarity : 0.004 0.069 3570 Dihedral : 5.324 72.621 2731 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.49 % Allowed : 4.49 % Favored : 95.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: -2.03 (0.16), residues: 2507 helix: 0.49 (0.20), residues: 668 sheet: -2.32 (0.19), residues: 664 loop : -1.78 (0.17), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP e 63 HIS 0.005 0.001 HIS R 77 PHE 0.019 0.001 PHE e 397 TYR 0.021 0.001 TYR a 312 ARG 0.004 0.000 ARG R 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 2255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 126 time to evaluate : 3.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 133 average time/residue: 0.6479 time to fit residues: 142.4913 Evaluate side-chains 126 residues out of total 2255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 3.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 CYS Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain R residue 103 PHE Chi-restraints excluded: chain a residue 37 ASP Chi-restraints excluded: chain d residue 562 THR Chi-restraints excluded: chain d residue 587 ILE Chi-restraints excluded: chain d residue 698 THR Chi-restraints excluded: chain e residue 173 MET Chi-restraints excluded: chain e residue 256 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 125 optimal weight: 0.0370 chunk 70 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 chunk 224 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 467 GLN ** d 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 399 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 20580 Z= 0.354 Angle : 0.566 8.487 27806 Z= 0.305 Chirality : 0.043 0.154 3134 Planarity : 0.004 0.053 3570 Dihedral : 5.201 70.689 2731 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 0.62 % Allowed : 6.27 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: -2.00 (0.16), residues: 2507 helix: 0.68 (0.20), residues: 669 sheet: -2.31 (0.19), residues: 707 loop : -1.82 (0.17), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP e 63 HIS 0.006 0.001 HIS R 48 PHE 0.016 0.001 PHE e 397 TYR 0.019 0.001 TYR a 312 ARG 0.003 0.000 ARG R 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 2255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 130 time to evaluate : 2.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 706 MET cc_start: 0.7947 (mmm) cc_final: 0.7702 (mmp) outliers start: 14 outliers final: 10 residues processed: 140 average time/residue: 0.5607 time to fit residues: 130.3222 Evaluate side-chains 132 residues out of total 2255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 122 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain R residue 103 PHE Chi-restraints excluded: chain a residue 37 ASP Chi-restraints excluded: chain a residue 119 SER Chi-restraints excluded: chain d residue 562 THR Chi-restraints excluded: chain d residue 581 MET Chi-restraints excluded: chain d residue 587 ILE Chi-restraints excluded: chain d residue 698 THR Chi-restraints excluded: chain d residue 986 ASP Chi-restraints excluded: chain e residue 256 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 223 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 227 optimal weight: 10.0000 chunk 240 optimal weight: 5.9990 chunk 118 optimal weight: 0.6980 chunk 215 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: