Starting phenix.real_space_refine on Tue Feb 20 13:09:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yys_11004/02_2024/6yys_11004.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yys_11004/02_2024/6yys_11004.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yys_11004/02_2024/6yys_11004.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yys_11004/02_2024/6yys_11004.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yys_11004/02_2024/6yys_11004.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yys_11004/02_2024/6yys_11004.pdb" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.025 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 2 6.06 5 Mg 1 5.21 5 S 98 5.16 5 C 17482 2.51 5 N 4963 2.21 5 O 5384 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 40": "NH1" <-> "NH2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A GLU 184": "OE1" <-> "OE2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "B PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ASP 72": "OD1" <-> "OD2" Residue "B ARG 186": "NH1" <-> "NH2" Residue "B ARG 205": "NH1" <-> "NH2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "C PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 172": "NH1" <-> "NH2" Residue "C ARG 199": "NH1" <-> "NH2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "C ASP 256": "OD1" <-> "OD2" Residue "C ASP 262": "OD1" <-> "OD2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C GLU 341": "OE1" <-> "OE2" Residue "C GLU 393": "OE1" <-> "OE2" Residue "C ARG 394": "NH1" <-> "NH2" Residue "C GLU 401": "OE1" <-> "OE2" Residue "C ARG 473": "NH1" <-> "NH2" Residue "C ARG 496": "NH1" <-> "NH2" Residue "C ARG 529": "NH1" <-> "NH2" Residue "C GLU 541": "OE1" <-> "OE2" Residue "C ARG 553": "NH1" <-> "NH2" Residue "C GLU 642": "OE1" <-> "OE2" Residue "C ASP 647": "OD1" <-> "OD2" Residue "C TYR 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 762": "NH1" <-> "NH2" Residue "C ARG 846": "NH1" <-> "NH2" Residue "C ARG 861": "NH1" <-> "NH2" Residue "C ARG 916": "NH1" <-> "NH2" Residue "C ASP 945": "OD1" <-> "OD2" Residue "C ARG 1058": "NH1" <-> "NH2" Residue "C ARG 1090": "NH1" <-> "NH2" Residue "C GLU 1095": "OE1" <-> "OE2" Residue "C GLU 1110": "OE1" <-> "OE2" Residue "C GLU 1127": "OE1" <-> "OE2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 69": "NH1" <-> "NH2" Residue "D ASP 119": "OD1" <-> "OD2" Residue "D TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 140": "OD1" <-> "OD2" Residue "D GLU 154": "OE1" <-> "OE2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D GLU 215": "OE1" <-> "OE2" Residue "D ASP 237": "OD1" <-> "OD2" Residue "D GLU 275": "OE1" <-> "OE2" Residue "D ARG 278": "NH1" <-> "NH2" Residue "D ARG 346": "NH1" <-> "NH2" Residue "D GLU 364": "OE1" <-> "OE2" Residue "D ARG 372": "NH1" <-> "NH2" Residue "D ASP 383": "OD1" <-> "OD2" Residue "D ARG 427": "NH1" <-> "NH2" Residue "D ARG 459": "NH1" <-> "NH2" Residue "D ARG 478": "NH1" <-> "NH2" Residue "D GLU 489": "OE1" <-> "OE2" Residue "D GLU 513": "OE1" <-> "OE2" Residue "D ARG 630": "NH1" <-> "NH2" Residue "D GLU 639": "OE1" <-> "OE2" Residue "D ARG 694": "NH1" <-> "NH2" Residue "D ARG 725": "NH1" <-> "NH2" Residue "D GLU 829": "OE1" <-> "OE2" Residue "D ARG 833": "NH1" <-> "NH2" Residue "D ASP 868": "OD1" <-> "OD2" Residue "D ARG 980": "NH1" <-> "NH2" Residue "D GLU 992": "OE1" <-> "OE2" Residue "D GLU 1034": "OE1" <-> "OE2" Residue "D GLU 1037": "OE1" <-> "OE2" Residue "D GLU 1057": "OE1" <-> "OE2" Residue "D ASP 1071": "OD1" <-> "OD2" Residue "D ARG 1084": "NH1" <-> "NH2" Residue "D ARG 1129": "NH1" <-> "NH2" Residue "D GLU 1130": "OE1" <-> "OE2" Residue "D ARG 1160": "NH1" <-> "NH2" Residue "D GLU 1188": "OE1" <-> "OE2" Residue "D ARG 1192": "NH1" <-> "NH2" Residue "D ARG 1193": "NH1" <-> "NH2" Residue "D ARG 1232": "NH1" <-> "NH2" Residue "D ARG 1269": "NH1" <-> "NH2" Residue "D ARG 1280": "NH1" <-> "NH2" Residue "E ASP 38": "OD1" <-> "OD2" Residue "E ARG 57": "NH1" <-> "NH2" Residue "E ARG 94": "NH1" <-> "NH2" Residue "H ARG 33": "NH1" <-> "NH2" Residue "H ARG 40": "NH1" <-> "NH2" Residue "H ARG 49": "NH1" <-> "NH2" Residue "H ARG 54": "NH1" <-> "NH2" Residue "H ARG 74": "NH1" <-> "NH2" Residue "H ARG 82": "NH1" <-> "NH2" Residue "H GLU 98": "OE1" <-> "OE2" Residue "H ARG 105": "NH1" <-> "NH2" Residue "H ARG 124": "NH1" <-> "NH2" Residue "H ARG 126": "NH1" <-> "NH2" Residue "H ARG 127": "NH1" <-> "NH2" Residue "H ARG 146": "NH1" <-> "NH2" Residue "H ARG 212": "NH1" <-> "NH2" Residue "H TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 226": "NH1" <-> "NH2" Residue "H GLU 278": "OE1" <-> "OE2" Residue "H ARG 296": "NH1" <-> "NH2" Residue "H GLU 298": "OE1" <-> "OE2" Residue "H ASP 325": "OD1" <-> "OD2" Residue "H ARG 338": "NH1" <-> "NH2" Residue "H TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 374": "NH1" <-> "NH2" Residue "H GLU 380": "OE1" <-> "OE2" Residue "H GLU 382": "OE1" <-> "OE2" Residue "H GLU 385": "OE1" <-> "OE2" Residue "H PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 421": "OE1" <-> "OE2" Residue "H GLU 454": "OE1" <-> "OE2" Residue "H ARG 477": "NH1" <-> "NH2" Residue "H GLU 484": "OE1" <-> "OE2" Residue "H ARG 501": "NH1" <-> "NH2" Residue "H GLU 504": "OE1" <-> "OE2" Residue "H ASP 506": "OD1" <-> "OD2" Residue "H ARG 544": "NH1" <-> "NH2" Residue "H ARG 559": "NH1" <-> "NH2" Residue "H ARG 560": "NH1" <-> "NH2" Residue "H GLU 605": "OE1" <-> "OE2" Residue "H GLU 648": "OE1" <-> "OE2" Residue "H GLU 667": "OE1" <-> "OE2" Residue "H GLU 672": "OE1" <-> "OE2" Residue "H GLU 680": "OE1" <-> "OE2" Residue "H ARG 683": "NH1" <-> "NH2" Residue "H ASP 687": "OD1" <-> "OD2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27930 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1700 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 209} Chain: "B" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1771 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 218} Chain: "C" Number of atoms: 8433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1089, 8433 Classifications: {'peptide': 1089} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1030} Chain breaks: 1 Chain: "D" Number of atoms: 9983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1278, 9983 Classifications: {'peptide': 1278} Link IDs: {'PCIS': 2, 'PTRANS': 55, 'TRANS': 1220} Chain: "E" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 646 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 76} Chain: "H" Number of atoms: 5394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5394 Classifications: {'peptide': 690} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 35, 'TRANS': 654} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18936 SG CYS D 890 32.412 58.908 85.500 1.00 20.18 S ATOM 19498 SG CYS D 967 35.112 61.401 86.427 1.00 17.64 S ATOM 19540 SG CYS D 974 33.241 59.760 89.058 1.00 16.19 S ATOM 19559 SG CYS D 977 35.392 57.643 87.140 1.00 15.04 S ATOM 12363 SG CYS D 60 35.972 123.749 100.192 1.00 71.56 S ATOM 12381 SG CYS D 62 36.317 128.117 100.110 1.00 72.47 S ATOM 12490 SG CYS D 75 32.830 125.496 98.665 1.00 69.70 S ATOM 12516 SG CYS D 78 36.162 125.705 96.570 1.00 72.83 S Time building chain proxies: 14.78, per 1000 atoms: 0.53 Number of scatterers: 27930 At special positions: 0 Unit cell: (130.483, 142.118, 181.18, 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 2 29.99 S 98 16.00 Mg 1 11.99 O 5384 8.00 N 4963 7.00 C 17482 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: 11.13 Conformation dependent library (CDL) restraints added in 5.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 974 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 977 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 890 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 967 " pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 62 " Number of angles added : 12 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6628 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 43 sheets defined 38.8% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.15 Creating SS restraints... Processing helix chain 'A' and resid 31 through 46 removed outlier: 3.999A pdb=" N ILE A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 106 through 110 removed outlier: 3.595A pdb=" N ILE A 110 " --> pdb=" O ALA A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 156 removed outlier: 3.805A pdb=" N SER A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 220 Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'B' and resid 34 through 45 Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 203 through 224 Processing helix chain 'C' and resid 49 through 57 Processing helix chain 'C' and resid 58 through 68 Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 109 through 117 Processing helix chain 'C' and resid 217 through 220 Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 235 through 243 Processing helix chain 'C' and resid 247 through 254 Processing helix chain 'C' and resid 260 through 273 Processing helix chain 'C' and resid 279 through 289 Processing helix chain 'C' and resid 300 through 312 Processing helix chain 'C' and resid 327 through 341 removed outlier: 3.994A pdb=" N ILE C 333 " --> pdb=" O VAL C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 396 removed outlier: 3.503A pdb=" N THR C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 Processing helix chain 'C' and resid 411 through 422 removed outlier: 3.541A pdb=" N VAL C 415 " --> pdb=" O ILE C 411 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA C 416 " --> pdb=" O ARG C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 441 Processing helix chain 'C' and resid 467 through 471 removed outlier: 3.818A pdb=" N TYR C 471 " --> pdb=" O PRO C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 528 Processing helix chain 'C' and resid 579 through 583 Processing helix chain 'C' and resid 587 through 591 Processing helix chain 'C' and resid 592 through 605 removed outlier: 3.969A pdb=" N GLN C 605 " --> pdb=" O ASN C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 628 Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 768 through 773 removed outlier: 3.792A pdb=" N ALA C 773 " --> pdb=" O GLU C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 891 through 895 Processing helix chain 'C' and resid 919 through 933 Processing helix chain 'C' and resid 944 through 948 Processing helix chain 'C' and resid 973 through 978 removed outlier: 3.563A pdb=" N GLY C 978 " --> pdb=" O GLY C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 983 removed outlier: 3.829A pdb=" N SER C 982 " --> pdb=" O GLY C 978 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR C 983 " --> pdb=" O LEU C 979 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 978 through 983' Processing helix chain 'C' and resid 1027 through 1031 Processing helix chain 'C' and resid 1060 through 1070 removed outlier: 3.663A pdb=" N TYR C1070 " --> pdb=" O ALA C1066 " (cutoff:3.500A) Processing helix chain 'C' and resid 1073 through 1082 Processing helix chain 'C' and resid 1089 through 1100 Processing helix chain 'C' and resid 1112 through 1121 Processing helix chain 'D' and resid 16 through 24 removed outlier: 3.765A pdb=" N ILE D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 40 removed outlier: 4.429A pdb=" N LYS D 40 " --> pdb=" O ARG D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'D' and resid 112 through 118 removed outlier: 3.666A pdb=" N TYR D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 130 removed outlier: 3.811A pdb=" N TYR D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 146 Processing helix chain 'D' and resid 149 through 187 removed outlier: 3.954A pdb=" N GLU D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 removed outlier: 4.165A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 247 Processing helix chain 'D' and resid 257 through 267 removed outlier: 3.595A pdb=" N ILE D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 284 Processing helix chain 'D' and resid 288 through 301 removed outlier: 4.425A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 313 Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 340 through 361 removed outlier: 4.792A pdb=" N ASP D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 382 removed outlier: 4.009A pdb=" N SER D 377 " --> pdb=" O MET D 373 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL D 378 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA D 380 " --> pdb=" O GLU D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 405 Processing helix chain 'D' and resid 447 through 452 removed outlier: 4.092A pdb=" N LEU D 451 " --> pdb=" O MET D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 469 through 479 Processing helix chain 'D' and resid 485 through 490 removed outlier: 3.939A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D 490 " --> pdb=" O VAL D 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 485 through 490' Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 578 through 589 Processing helix chain 'D' and resid 601 through 605 removed outlier: 4.060A pdb=" N LYS D 604 " --> pdb=" O ALA D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 624 removed outlier: 3.545A pdb=" N ALA D 618 " --> pdb=" O SER D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 643 through 651 removed outlier: 4.202A pdb=" N GLN D 649 " --> pdb=" O ASP D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 674 removed outlier: 3.525A pdb=" N VAL D 670 " --> pdb=" O THR D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 703 Processing helix chain 'D' and resid 704 through 725 removed outlier: 3.892A pdb=" N VAL D 708 " --> pdb=" O PRO D 704 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR D 724 " --> pdb=" O PHE D 720 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 762 removed outlier: 3.963A pdb=" N GLU D 751 " --> pdb=" O ARG D 747 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU D 756 " --> pdb=" O ALA D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 765 through 777 Processing helix chain 'D' and resid 780 through 792 Processing helix chain 'D' and resid 796 through 804 removed outlier: 4.142A pdb=" N VAL D 802 " --> pdb=" O ILE D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 818 removed outlier: 3.582A pdb=" N THR D 813 " --> pdb=" O ASN D 809 " (cutoff:3.500A) Processing helix chain 'D' and resid 844 through 857 removed outlier: 3.619A pdb=" N HIS D 853 " --> pdb=" O PHE D 849 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLY D 854 " --> pdb=" O ILE D 850 " (cutoff:3.500A) Processing helix chain 'D' and resid 857 through 880 removed outlier: 4.241A pdb=" N ASP D 861 " --> pdb=" O LYS D 857 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR D 862 " --> pdb=" O GLY D 858 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA D 863 " --> pdb=" O LEU D 859 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR D 866 " --> pdb=" O THR D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 919 Processing helix chain 'D' and resid 944 through 954 Processing helix chain 'D' and resid 975 through 979 Processing helix chain 'D' and resid 994 through 1004 removed outlier: 3.550A pdb=" N ALA D 998 " --> pdb=" O VAL D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1005 through 1009 removed outlier: 3.692A pdb=" N LEU D1009 " --> pdb=" O GLY D1006 " (cutoff:3.500A) Processing helix chain 'D' and resid 1020 through 1024 removed outlier: 3.533A pdb=" N ASP D1024 " --> pdb=" O GLY D1021 " (cutoff:3.500A) Processing helix chain 'D' and resid 1028 through 1038 Processing helix chain 'D' and resid 1118 through 1126 Processing helix chain 'D' and resid 1129 through 1146 removed outlier: 3.726A pdb=" N ILE D1133 " --> pdb=" O ARG D1129 " (cutoff:3.500A) Processing helix chain 'D' and resid 1151 through 1161 removed outlier: 4.301A pdb=" N ILE D1155 " --> pdb=" O HIS D1151 " (cutoff:3.500A) Processing helix chain 'D' and resid 1184 through 1193 Processing helix chain 'D' and resid 1210 through 1217 removed outlier: 3.510A pdb=" N LEU D1216 " --> pdb=" O THR D1212 " (cutoff:3.500A) Processing helix chain 'D' and resid 1221 through 1227 removed outlier: 3.870A pdb=" N ALA D1225 " --> pdb=" O TRP D1221 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE D1227 " --> pdb=" O SER D1223 " (cutoff:3.500A) Processing helix chain 'D' and resid 1229 through 1241 Processing helix chain 'D' and resid 1251 through 1256 Processing helix chain 'D' and resid 1265 through 1270 Processing helix chain 'D' and resid 1276 through 1281 Processing helix chain 'E' and resid 30 through 34 Processing helix chain 'E' and resid 39 through 43 removed outlier: 3.585A pdb=" N SER E 42 " --> pdb=" O GLU E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 67 removed outlier: 4.197A pdb=" N ARG E 57 " --> pdb=" O TYR E 53 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN E 67 " --> pdb=" O ASP E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 98 Processing helix chain 'H' and resid 3 through 41 Processing helix chain 'H' and resid 45 through 67 Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.659A pdb=" N ARG H 110 " --> pdb=" O PRO H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 188 removed outlier: 3.615A pdb=" N ILE H 179 " --> pdb=" O ILE H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 220 Processing helix chain 'H' and resid 235 through 239 removed outlier: 3.797A pdb=" N PHE H 238 " --> pdb=" O THR H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 246 Processing helix chain 'H' and resid 246 through 251 Processing helix chain 'H' and resid 275 through 281 removed outlier: 3.990A pdb=" N VAL H 279 " --> pdb=" O GLU H 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 295 removed outlier: 4.241A pdb=" N ASP H 287 " --> pdb=" O LEU H 283 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL H 288 " --> pdb=" O LYS H 284 " (cutoff:3.500A) Processing helix chain 'H' and resid 316 through 329 Processing helix chain 'H' and resid 333 through 355 removed outlier: 4.898A pdb=" N ALA H 339 " --> pdb=" O ASN H 335 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLU H 340 " --> pdb=" O GLU H 336 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU H 351 " --> pdb=" O TYR H 347 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ARG H 352 " --> pdb=" O VAL H 348 " (cutoff:3.500A) Processing helix chain 'H' and resid 372 through 377 Processing helix chain 'H' and resid 384 through 392 Processing helix chain 'H' and resid 401 through 409 removed outlier: 3.772A pdb=" N LEU H 407 " --> pdb=" O VAL H 403 " (cutoff:3.500A) Processing helix chain 'H' and resid 411 through 417 removed outlier: 4.342A pdb=" N ARG H 415 " --> pdb=" O HIS H 411 " (cutoff:3.500A) Processing helix chain 'H' and resid 435 through 447 removed outlier: 3.766A pdb=" N VAL H 443 " --> pdb=" O LEU H 439 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP H 444 " --> pdb=" O ASP H 440 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY H 447 " --> pdb=" O VAL H 443 " (cutoff:3.500A) Processing helix chain 'H' and resid 454 through 474 removed outlier: 3.729A pdb=" N ARG H 458 " --> pdb=" O GLU H 454 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET H 474 " --> pdb=" O VAL H 470 " (cutoff:3.500A) Processing helix chain 'H' and resid 494 through 500 Processing helix chain 'H' and resid 509 through 516 removed outlier: 3.517A pdb=" N ALA H 516 " --> pdb=" O GLU H 512 " (cutoff:3.500A) Processing helix chain 'H' and resid 529 through 533 removed outlier: 3.643A pdb=" N GLU H 532 " --> pdb=" O GLU H 529 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU H 533 " --> pdb=" O ALA H 530 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 529 through 533' Processing helix chain 'H' and resid 534 through 545 Processing helix chain 'H' and resid 567 through 573 removed outlier: 3.813A pdb=" N MET H 571 " --> pdb=" O SER H 567 " (cutoff:3.500A) Processing helix chain 'H' and resid 592 through 603 Processing helix chain 'H' and resid 632 through 645 removed outlier: 3.946A pdb=" N ALA H 645 " --> pdb=" O VAL H 641 " (cutoff:3.500A) Processing helix chain 'H' and resid 680 through 688 removed outlier: 4.299A pdb=" N GLY H 688 " --> pdb=" O ILE H 684 " (cutoff:3.500A) Processing helix chain 'H' and resid 690 through 700 removed outlier: 3.563A pdb=" N GLU H 694 " --> pdb=" O ARG H 690 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA H 698 " --> pdb=" O GLU H 694 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR H 700 " --> pdb=" O TYR H 696 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 6.203A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 94 Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 94 removed outlier: 7.725A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 12 removed outlier: 6.784A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 98 removed outlier: 7.761A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 86 removed outlier: 3.728A pdb=" N THR B 117 " --> pdb=" O SER B 86 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 104 through 106 removed outlier: 3.504A pdb=" N ALA B 126 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'C' and resid 30 through 31 removed outlier: 6.554A pdb=" N VAL C 30 " --> pdb=" O ALA C 964 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 87 through 88 removed outlier: 6.595A pdb=" N PHE C 125 " --> pdb=" O PRO C 101 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE C 103 " --> pdb=" O PRO C 123 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU C 137 " --> pdb=" O ASN C 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 87 through 88 removed outlier: 6.595A pdb=" N PHE C 125 " --> pdb=" O PRO C 101 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE C 103 " --> pdb=" O PRO C 123 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ALA C 122 " --> pdb=" O ASP C 147 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP C 147 " --> pdb=" O ALA C 122 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU C 124 " --> pdb=" O MET C 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 157 through 159 Processing sheet with id=AB6, first strand: chain 'C' and resid 367 through 370 removed outlier: 3.822A pdb=" N SER C 168 " --> pdb=" O ARG C 445 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 175 through 177 Processing sheet with id=AB8, first strand: chain 'C' and resid 175 through 177 removed outlier: 4.090A pdb=" N HIS C 191 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 207 " --> pdb=" O HIS C 191 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 345 through 347 Processing sheet with id=AC1, first strand: chain 'C' and resid 496 through 497 removed outlier: 5.364A pdb=" N GLN C 518 " --> pdb=" O LYS C 509 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 496 through 497 Processing sheet with id=AC3, first strand: chain 'C' and resid 549 through 552 Processing sheet with id=AC4, first strand: chain 'C' and resid 633 through 634 removed outlier: 6.466A pdb=" N VAL C 633 " --> pdb=" O ILE C 693 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 639 through 644 removed outlier: 5.335A pdb=" N ILE C 641 " --> pdb=" O MET C 652 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N MET C 652 " --> pdb=" O ILE C 641 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 998 through 999 removed outlier: 6.812A pdb=" N ILE C 726 " --> pdb=" O LYS C 888 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N LEU C 890 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU C 728 " --> pdb=" O LEU C 890 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR C1015 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 740 through 751 removed outlier: 3.692A pdb=" N GLU C 858 " --> pdb=" O ALA C 750 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ASN C 857 " --> pdb=" O SER C 845 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N SER C 845 " --> pdb=" O ASN C 857 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU C 859 " --> pdb=" O VAL C 843 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL C 843 " --> pdb=" O LEU C 859 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG C 861 " --> pdb=" O ILE C 841 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE C 841 " --> pdb=" O ARG C 861 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR C 863 " --> pdb=" O ILE C 839 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LYS C 867 " --> pdb=" O SER C 835 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N SER C 835 " --> pdb=" O LYS C 867 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY C 836 " --> pdb=" O VAL C 787 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 759 through 760 Processing sheet with id=AC9, first strand: chain 'C' and resid 792 through 794 removed outlier: 6.965A pdb=" N LEU C 828 " --> pdb=" O LEU C 793 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 935 through 936 Processing sheet with id=AD2, first strand: chain 'C' and resid 1033 through 1035 removed outlier: 8.182A pdb=" N ALA D 521 " --> pdb=" O PRO D 444 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1124 through 1128 removed outlier: 3.510A pdb=" N GLU C1127 " --> pdb=" O ARG D 11 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ARG D 11 " --> pdb=" O GLU C1127 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 94 through 95 Processing sheet with id=AD5, first strand: chain 'D' and resid 234 through 235 removed outlier: 3.559A pdb=" N TYR D 134 " --> pdb=" O ILE D 235 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AD7, first strand: chain 'D' and resid 885 through 887 Processing sheet with id=AD8, first strand: chain 'D' and resid 896 through 898 Processing sheet with id=AD9, first strand: chain 'D' and resid 902 through 903 Processing sheet with id=AE1, first strand: chain 'D' and resid 928 through 929 removed outlier: 3.647A pdb=" N ILE D 937 " --> pdb=" O ALA D 928 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1076 through 1082 removed outlier: 4.523A pdb=" N LYS D1080 " --> pdb=" O PHE D1063 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N PHE D1063 " --> pdb=" O LYS D1080 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1181 through 1183 removed outlier: 4.736A pdb=" N ARG D1165 " --> pdb=" O VAL D1207 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE D1169 " --> pdb=" O ALA D1203 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ALA D1203 " --> pdb=" O ILE D1169 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1272 through 1275 Processing sheet with id=AE5, first strand: chain 'H' and resid 98 through 103 removed outlier: 16.519A pdb=" N GLU H 98 " --> pdb=" O GLY H 86 " (cutoff:3.500A) removed outlier: 13.025A pdb=" N LEU H 88 " --> pdb=" O GLU H 98 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU H 100 " --> pdb=" O LEU H 88 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE H 90 " --> pdb=" O LEU H 100 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU H 102 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 11.901A pdb=" N ASP H 92 " --> pdb=" O LEU H 102 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU H 83 " --> pdb=" O ARG H 74 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ARG H 74 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE H 85 " --> pdb=" O PHE H 72 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE H 72 " --> pdb=" O PHE H 129 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ARG H 74 " --> pdb=" O ARG H 127 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ARG H 126 " --> pdb=" O ASP H 141 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASP H 141 " --> pdb=" O ARG H 126 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLN H 128 " --> pdb=" O PHE H 139 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE H 139 " --> pdb=" O GLN H 128 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N HIS H 130 " --> pdb=" O VAL H 137 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 256 through 257 removed outlier: 7.702A pdb=" N MET H 257 " --> pdb=" O VAL H 229 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL H 231 " --> pdb=" O MET H 257 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU H 230 " --> pdb=" O VAL H 526 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'H' and resid 624 through 627 removed outlier: 3.916A pdb=" N TRP H 624 " --> pdb=" O LEU H 706 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL H 708 " --> pdb=" O TRP H 624 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ASP H 674 " --> pdb=" O ARG H 705 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N GLY H 707 " --> pdb=" O ASP H 674 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL H 676 " --> pdb=" O GLY H 707 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N LEU H 709 " --> pdb=" O VAL H 676 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL H 678 " --> pdb=" O LEU H 709 " (cutoff:3.500A) 1098 hydrogen bonds defined for protein. 3060 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: 11.82 Time building geometry restraints manager: 11.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9690 1.34 - 1.47: 5827 1.47 - 1.59: 12718 1.59 - 1.71: 0 1.71 - 1.83: 174 Bond restraints: 28409 Sorted by residual: bond pdb=" N MET H 1 " pdb=" CA MET H 1 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.38e+00 bond pdb=" N THR C 479 " pdb=" CA THR C 479 " ideal model delta sigma weight residual 1.457 1.433 0.024 1.41e-02 5.03e+03 2.99e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.63e+00 bond pdb=" C GLU C 613 " pdb=" N ALA C 614 " ideal model delta sigma weight residual 1.329 1.288 0.040 3.03e-02 1.09e+03 1.76e+00 ... (remaining 28404 not shown) Histogram of bond angle deviations from ideal: 97.56 - 104.86: 593 104.86 - 112.15: 13968 112.15 - 119.45: 9668 119.45 - 126.75: 13944 126.75 - 134.04: 335 Bond angle restraints: 38508 Sorted by residual: angle pdb=" N LYS C 295 " pdb=" CA LYS C 295 " pdb=" C LYS C 295 " ideal model delta sigma weight residual 114.75 110.04 4.71 1.26e+00 6.30e-01 1.40e+01 angle pdb=" N THR C 479 " pdb=" CA THR C 479 " pdb=" C THR C 479 " ideal model delta sigma weight residual 109.81 102.81 7.00 2.21e+00 2.05e-01 1.00e+01 angle pdb=" C ILE C 919 " pdb=" CA ILE C 919 " pdb=" CB ILE C 919 " ideal model delta sigma weight residual 111.29 106.47 4.82 1.64e+00 3.72e-01 8.63e+00 angle pdb=" N LEU D 579 " pdb=" CA LEU D 579 " pdb=" C LEU D 579 " ideal model delta sigma weight residual 111.02 114.24 -3.22 1.22e+00 6.72e-01 6.97e+00 angle pdb=" CA TYR E 53 " pdb=" CB TYR E 53 " pdb=" CG TYR E 53 " ideal model delta sigma weight residual 113.90 118.52 -4.62 1.80e+00 3.09e-01 6.57e+00 ... (remaining 38503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 15744 17.90 - 35.80: 1372 35.80 - 53.71: 209 53.71 - 71.61: 40 71.61 - 89.51: 23 Dihedral angle restraints: 17388 sinusoidal: 7087 harmonic: 10301 Sorted by residual: dihedral pdb=" CA ASP D 605 " pdb=" C ASP D 605 " pdb=" N ALA D 606 " pdb=" CA ALA D 606 " ideal model delta harmonic sigma weight residual 180.00 152.62 27.38 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA GLN C 433 " pdb=" C GLN C 433 " pdb=" N ASN C 434 " pdb=" CA ASN C 434 " ideal model delta harmonic sigma weight residual 180.00 154.48 25.52 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA SER C 573 " pdb=" C SER C 573 " pdb=" N PRO C 574 " pdb=" CA PRO C 574 " ideal model delta harmonic sigma weight residual 180.00 155.66 24.34 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 17385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2483 0.030 - 0.061: 1231 0.061 - 0.091: 416 0.091 - 0.122: 211 0.122 - 0.152: 31 Chirality restraints: 4372 Sorted by residual: chirality pdb=" CA PRO D 577 " pdb=" N PRO D 577 " pdb=" C PRO D 577 " pdb=" CB PRO D 577 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" CA ILE D 51 " pdb=" N ILE D 51 " pdb=" C ILE D 51 " pdb=" CB ILE D 51 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA PRO H 107 " pdb=" N PRO H 107 " pdb=" C PRO H 107 " pdb=" CB PRO H 107 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 4369 not shown) Planarity restraints: 5099 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 607 " 0.039 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO C 608 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 608 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 608 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 680 " -0.038 5.00e-02 4.00e+02 5.83e-02 5.43e+00 pdb=" N PRO D 681 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 681 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 681 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 110 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO H 111 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO H 111 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 111 " 0.032 5.00e-02 4.00e+02 ... (remaining 5096 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 202 2.52 - 3.12: 22373 3.12 - 3.71: 40094 3.71 - 4.31: 60119 4.31 - 4.90: 101363 Nonbonded interactions: 224151 Sorted by model distance: nonbonded pdb=" OH TYR D 599 " pdb=" OE1 GLU D 608 " model vdw 1.926 2.440 nonbonded pdb=" OG SER A 210 " pdb=" O SER B 229 " model vdw 2.000 2.440 nonbonded pdb=" OG1 THR H 77 " pdb=" OD1 ASP H 79 " model vdw 2.058 2.440 nonbonded pdb=" OH TYR C 335 " pdb=" O PRO C 355 " model vdw 2.084 2.440 nonbonded pdb=" OG SER C 173 " pdb=" O ASN C 366 " model vdw 2.092 2.440 ... (remaining 224146 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 224) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.830 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: 0.000 Extract box with map and model: 14.470 Check model and map are aligned: 0.230 Set scattering table: 0.280 Process input model: 80.140 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.130 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 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 0.048 28409 Z= 0.329 Angle : 0.656 8.944 38508 Z= 0.363 Chirality : 0.044 0.152 4372 Planarity : 0.006 0.060 5099 Dihedral : 13.863 89.510 10760 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.82 % Favored : 91.15 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % 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: -4.90 (0.11), residues: 3581 helix: -3.20 (0.11), residues: 1242 sheet: -1.90 (0.23), residues: 408 loop : -3.72 (0.11), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 61 HIS 0.013 0.001 HIS C 470 PHE 0.030 0.002 PHE D1063 TYR 0.037 0.002 TYR E 53 ARG 0.008 0.001 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 3.122 Fit side-chains 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: 344 average time/residue: 0.5175 time to fit residues: 256.9172 Evaluate side-chains 168 residues out of total 2997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 3.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 301 optimal weight: 3.9990 chunk 270 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 182 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 chunk 279 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 170 optimal weight: 9.9990 chunk 208 optimal weight: 0.9980 chunk 324 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 151 GLN B 36 ASN B 151 GLN B 152 ASN ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 ASN D 145 HIS D 410 GLN D 494 HIS D 600 GLN D 765 ASN D1247 ASN H 64 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28409 Z= 0.233 Angle : 0.641 11.114 38508 Z= 0.330 Chirality : 0.046 0.245 4372 Planarity : 0.005 0.058 5099 Dihedral : 4.940 23.534 3949 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.93 % Allowed : 7.21 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % 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: -2.76 (0.13), residues: 3581 helix: -1.02 (0.14), residues: 1290 sheet: -1.35 (0.24), residues: 413 loop : -2.61 (0.12), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 624 HIS 0.013 0.001 HIS D 145 PHE 0.024 0.002 PHE H 640 TYR 0.031 0.002 TYR E 53 ARG 0.007 0.001 ARG D 89 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 196 time to evaluate : 2.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 92 MET cc_start: 0.3542 (OUTLIER) cc_final: 0.3208 (ptm) outliers start: 28 outliers final: 16 residues processed: 220 average time/residue: 0.4199 time to fit residues: 145.5210 Evaluate side-chains 175 residues out of total 2997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 158 time to evaluate : 3.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 945 ASP Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain H residue 633 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 180 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 269 optimal weight: 7.9990 chunk 220 optimal weight: 0.5980 chunk 89 optimal weight: 0.0270 chunk 324 optimal weight: 10.0000 chunk 350 optimal weight: 20.0000 chunk 289 optimal weight: 8.9990 chunk 322 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 260 optimal weight: 3.9990 overall best weight: 2.1244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 238 GLN D 145 HIS D 932 ASN H 627 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28409 Z= 0.248 Angle : 0.588 9.672 38508 Z= 0.302 Chirality : 0.044 0.149 4372 Planarity : 0.005 0.058 5099 Dihedral : 4.608 21.758 3949 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.64 % Allowed : 9.85 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % 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: -1.80 (0.13), residues: 3581 helix: -0.15 (0.14), residues: 1314 sheet: -0.95 (0.25), residues: 394 loop : -2.07 (0.13), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 624 HIS 0.007 0.001 HIS C 470 PHE 0.017 0.002 PHE C 364 TYR 0.026 0.001 TYR E 53 ARG 0.013 0.001 ARG H 705 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 180 time to evaluate : 3.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 327 MET cc_start: 0.3127 (ttp) cc_final: 0.2809 (mtm) REVERT: D 1016 GLN cc_start: 0.5933 (mp10) cc_final: 0.5713 (mp10) outliers start: 49 outliers final: 27 residues processed: 219 average time/residue: 0.4212 time to fit residues: 145.6218 Evaluate side-chains 186 residues out of total 2997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 159 time to evaluate : 3.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 945 ASP Chi-restraints excluded: chain C residue 1114 VAL Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain D residue 1263 THR Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain H residue 307 ASP Chi-restraints excluded: chain H residue 348 VAL Chi-restraints excluded: chain H residue 354 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 320 optimal weight: 10.0000 chunk 244 optimal weight: 0.9990 chunk 168 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 154 optimal weight: 9.9990 chunk 218 optimal weight: 4.9990 chunk 325 optimal weight: 9.9990 chunk 345 optimal weight: 9.9990 chunk 170 optimal weight: 5.9990 chunk 308 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 GLN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN C 603 GLN C 766 ASN ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN D 245 GLN D 352 ASN D 375 GLN ** D 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 505 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 28409 Z= 0.528 Angle : 0.729 9.593 38508 Z= 0.376 Chirality : 0.049 0.217 4372 Planarity : 0.006 0.074 5099 Dihedral : 5.143 23.605 3949 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 2.40 % Allowed : 11.72 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % 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: -1.79 (0.13), residues: 3581 helix: -0.32 (0.14), residues: 1335 sheet: -0.86 (0.25), residues: 396 loop : -1.95 (0.13), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 370 HIS 0.011 0.002 HIS C 470 PHE 0.029 0.003 PHE C1112 TYR 0.029 0.002 TYR E 53 ARG 0.010 0.001 ARG D 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 165 time to evaluate : 3.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1119 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8935 (mp) REVERT: D 687 MET cc_start: 0.7664 (mmp) cc_final: 0.7318 (mmp) outliers start: 72 outliers final: 41 residues processed: 224 average time/residue: 0.4110 time to fit residues: 147.2788 Evaluate side-chains 198 residues out of total 2997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 156 time to evaluate : 3.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 945 ASP Chi-restraints excluded: chain C residue 1114 VAL Chi-restraints excluded: chain C residue 1119 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 809 ASN Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain H residue 307 ASP Chi-restraints excluded: chain H residue 348 VAL Chi-restraints excluded: chain H residue 354 VAL Chi-restraints excluded: chain H residue 663 VAL Chi-restraints excluded: chain H residue 678 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 287 optimal weight: 4.9990 chunk 195 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 256 optimal weight: 0.1980 chunk 142 optimal weight: 4.9990 chunk 294 optimal weight: 2.9990 chunk 238 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 176 optimal weight: 10.0000 chunk 309 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 GLN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 600 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 28409 Z= 0.160 Angle : 0.553 10.496 38508 Z= 0.283 Chirality : 0.043 0.148 4372 Planarity : 0.004 0.058 5099 Dihedral : 4.579 23.070 3949 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.40 % Allowed : 12.95 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % 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 (0.14), residues: 3581 helix: 0.41 (0.15), residues: 1313 sheet: -0.67 (0.24), residues: 417 loop : -1.65 (0.13), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 361 HIS 0.005 0.001 HIS D1151 PHE 0.020 0.001 PHE H 640 TYR 0.015 0.001 TYR E 53 ARG 0.004 0.000 ARG D 247 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 168 time to evaluate : 2.982 Fit side-chains revert: symmetry clash REVERT: D 687 MET cc_start: 0.7577 (mmp) cc_final: 0.7083 (mmp) outliers start: 42 outliers final: 25 residues processed: 205 average time/residue: 0.4195 time to fit residues: 136.0632 Evaluate side-chains 176 residues out of total 2997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 151 time to evaluate : 3.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain D residue 1092 HIS Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain H residue 307 ASP Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 663 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 116 optimal weight: 2.9990 chunk 310 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 202 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 345 optimal weight: 10.0000 chunk 286 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 181 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 ASN C 603 GLN D 465 HIS E 66 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 28409 Z= 0.483 Angle : 0.678 10.377 38508 Z= 0.348 Chirality : 0.048 0.203 4372 Planarity : 0.005 0.069 5099 Dihedral : 4.895 22.298 3949 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.20 % Allowed : 13.19 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % 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: -1.29 (0.13), residues: 3581 helix: 0.16 (0.14), residues: 1324 sheet: -0.62 (0.24), residues: 428 loop : -1.70 (0.13), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 361 HIS 0.008 0.001 HIS C 470 PHE 0.019 0.002 PHE D 226 TYR 0.024 0.002 TYR E 53 ARG 0.006 0.001 ARG D1192 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 156 time to evaluate : 3.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 327 MET cc_start: 0.3276 (ttp) cc_final: 0.2715 (mtm) REVERT: D 687 MET cc_start: 0.7558 (mmp) cc_final: 0.7275 (mmp) outliers start: 66 outliers final: 49 residues processed: 213 average time/residue: 0.4052 time to fit residues: 138.9445 Evaluate side-chains 198 residues out of total 2997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 149 time to evaluate : 3.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 945 ASP Chi-restraints excluded: chain C residue 1114 VAL Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 1197 GLU Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain H residue 307 ASP Chi-restraints excluded: chain H residue 348 VAL Chi-restraints excluded: chain H residue 354 VAL Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 663 VAL Chi-restraints excluded: chain H residue 678 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 333 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 196 optimal weight: 0.9990 chunk 252 optimal weight: 0.9990 chunk 195 optimal weight: 2.9990 chunk 290 optimal weight: 0.9990 chunk 192 optimal weight: 7.9990 chunk 344 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 209 optimal weight: 0.7980 chunk 158 optimal weight: 5.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN B 151 GLN C 603 GLN D 600 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28409 Z= 0.174 Angle : 0.551 11.245 38508 Z= 0.279 Chirality : 0.043 0.190 4372 Planarity : 0.004 0.058 5099 Dihedral : 4.497 22.828 3949 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.64 % Allowed : 14.16 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % 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: -0.83 (0.14), residues: 3581 helix: 0.60 (0.15), residues: 1327 sheet: -0.54 (0.24), residues: 427 loop : -1.45 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 361 HIS 0.005 0.001 HIS D1151 PHE 0.029 0.001 PHE H 640 TYR 0.015 0.001 TYR H 408 ARG 0.004 0.000 ARG D1205 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 156 time to evaluate : 3.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 327 MET cc_start: 0.3242 (ttp) cc_final: 0.2633 (mtm) REVERT: D 687 MET cc_start: 0.7538 (mmp) cc_final: 0.7083 (mmp) outliers start: 49 outliers final: 39 residues processed: 199 average time/residue: 0.3926 time to fit residues: 127.9286 Evaluate side-chains 188 residues out of total 2997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 149 time to evaluate : 3.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 1114 VAL Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain D residue 1092 HIS Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain H residue 307 ASP Chi-restraints excluded: chain H residue 310 ASP Chi-restraints excluded: chain H residue 354 VAL Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 663 VAL Chi-restraints excluded: chain H residue 678 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 212 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 205 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 67 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 218 optimal weight: 3.9990 chunk 234 optimal weight: 7.9990 chunk 170 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 270 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 GLN D 600 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 28409 Z= 0.257 Angle : 0.576 11.134 38508 Z= 0.291 Chirality : 0.044 0.193 4372 Planarity : 0.004 0.058 5099 Dihedral : 4.468 20.837 3949 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 1.87 % Allowed : 14.26 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % 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: -0.72 (0.14), residues: 3581 helix: 0.69 (0.15), residues: 1322 sheet: -0.42 (0.24), residues: 449 loop : -1.40 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP H 361 HIS 0.006 0.001 HIS D1151 PHE 0.026 0.001 PHE H 640 TYR 0.018 0.001 TYR E 53 ARG 0.007 0.000 ARG D 247 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 152 time to evaluate : 3.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 327 MET cc_start: 0.3416 (ttp) cc_final: 0.2584 (mtm) REVERT: D 687 MET cc_start: 0.7490 (mmp) cc_final: 0.7110 (mmp) outliers start: 56 outliers final: 51 residues processed: 200 average time/residue: 0.3921 time to fit residues: 128.4009 Evaluate side-chains 200 residues out of total 2997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 149 time to evaluate : 3.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 1114 VAL Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain D residue 1092 HIS Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain H residue 307 ASP Chi-restraints excluded: chain H residue 310 ASP Chi-restraints excluded: chain H residue 348 VAL Chi-restraints excluded: chain H residue 354 VAL Chi-restraints excluded: chain H residue 378 VAL Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 663 VAL Chi-restraints excluded: chain H residue 678 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 313 optimal weight: 5.9990 chunk 329 optimal weight: 0.7980 chunk 300 optimal weight: 7.9990 chunk 320 optimal weight: 7.9990 chunk 192 optimal weight: 6.9990 chunk 139 optimal weight: 0.8980 chunk 251 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 289 optimal weight: 7.9990 chunk 303 optimal weight: 4.9990 chunk 319 optimal weight: 2.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 28409 Z= 0.306 Angle : 0.600 12.173 38508 Z= 0.303 Chirality : 0.044 0.193 4372 Planarity : 0.005 0.060 5099 Dihedral : 4.560 22.890 3949 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.00 % Allowed : 14.59 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % 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: -0.71 (0.14), residues: 3581 helix: 0.66 (0.15), residues: 1324 sheet: -0.38 (0.24), residues: 442 loop : -1.37 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP H 361 HIS 0.007 0.001 HIS D1151 PHE 0.024 0.002 PHE H 640 TYR 0.020 0.001 TYR E 53 ARG 0.007 0.000 ARG D 247 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 155 time to evaluate : 3.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 327 MET cc_start: 0.3560 (ttp) cc_final: 0.2685 (mtm) REVERT: D 687 MET cc_start: 0.7498 (mmp) cc_final: 0.7127 (mmp) outliers start: 60 outliers final: 54 residues processed: 205 average time/residue: 0.4268 time to fit residues: 141.7015 Evaluate side-chains 202 residues out of total 2997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 148 time to evaluate : 3.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 945 ASP Chi-restraints excluded: chain C residue 1114 VAL Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain D residue 1092 HIS Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain H residue 307 ASP Chi-restraints excluded: chain H residue 310 ASP Chi-restraints excluded: chain H residue 348 VAL Chi-restraints excluded: chain H residue 354 VAL Chi-restraints excluded: chain H residue 378 VAL Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 663 VAL Chi-restraints excluded: chain H residue 678 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 210 optimal weight: 0.6980 chunk 339 optimal weight: 6.9990 chunk 206 optimal weight: 4.9990 chunk 160 optimal weight: 0.9980 chunk 235 optimal weight: 4.9990 chunk 355 optimal weight: 5.9990 chunk 327 optimal weight: 0.3980 chunk 283 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 218 optimal weight: 7.9990 chunk 173 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 GLN ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 600 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28409 Z= 0.177 Angle : 0.554 13.402 38508 Z= 0.277 Chirality : 0.043 0.180 4372 Planarity : 0.004 0.057 5099 Dihedral : 4.331 21.302 3949 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.57 % Allowed : 15.16 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % 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: -0.46 (0.14), residues: 3581 helix: 0.88 (0.15), residues: 1325 sheet: -0.24 (0.25), residues: 439 loop : -1.23 (0.14), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP H 361 HIS 0.005 0.001 HIS D1151 PHE 0.024 0.001 PHE H 640 TYR 0.017 0.001 TYR D 248 ARG 0.005 0.000 ARG D 247 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 159 time to evaluate : 3.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 327 MET cc_start: 0.3341 (ttp) cc_final: 0.2489 (mtm) REVERT: D 687 MET cc_start: 0.7517 (mmp) cc_final: 0.7075 (mmp) outliers start: 47 outliers final: 44 residues processed: 200 average time/residue: 0.3845 time to fit residues: 125.0306 Evaluate side-chains 192 residues out of total 2997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 148 time to evaluate : 3.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 1114 VAL Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain D residue 1092 HIS Chi-restraints excluded: chain H residue 307 ASP Chi-restraints excluded: chain H residue 310 ASP Chi-restraints excluded: chain H residue 354 VAL Chi-restraints excluded: chain H residue 378 VAL Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 663 VAL Chi-restraints excluded: chain H residue 678 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 224 optimal weight: 4.9990 chunk 301 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 261 optimal weight: 0.0570 chunk 41 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 283 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 291 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 overall best weight: 1.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 600 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.074228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.055900 restraints weight = 87728.680| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.74 r_work: 0.2983 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 28409 Z= 0.171 Angle : 0.546 12.841 38508 Z= 0.273 Chirality : 0.043 0.193 4372 Planarity : 0.004 0.058 5099 Dihedral : 4.228 20.553 3949 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.57 % Allowed : 15.29 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % 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 (0.14), residues: 3581 helix: 1.02 (0.15), residues: 1325 sheet: -0.19 (0.25), residues: 425 loop : -1.12 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP H 361 HIS 0.005 0.001 HIS D1151 PHE 0.023 0.001 PHE H 640 TYR 0.016 0.001 TYR E 53 ARG 0.006 0.000 ARG D 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5356.40 seconds wall clock time: 98 minutes 48.03 seconds (5928.03 seconds total)