Starting phenix.real_space_refine on Sun Mar 17 11:18:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foj_29351/03_2024/8foj_29351_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foj_29351/03_2024/8foj_29351.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foj_29351/03_2024/8foj_29351.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foj_29351/03_2024/8foj_29351.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foj_29351/03_2024/8foj_29351_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foj_29351/03_2024/8foj_29351_updated.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 Fe 4 7.16 5 P 21 5.49 5 S 95 5.16 5 C 11100 2.51 5 N 2971 2.21 5 O 3347 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 702": "OE1" <-> "OE2" Residue "1 GLU 798": "OE1" <-> "OE2" Residue "1 PHE 880": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 888": "OE1" <-> "OE2" Residue "1 GLU 927": "OE1" <-> "OE2" Residue "1 TYR 951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 961": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 1112": "OD1" <-> "OD2" Residue "1 PHE 1170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 1291": "OD1" <-> "OD2" Residue "1 GLU 1318": "OE1" <-> "OE2" Residue "1 GLU 1432": "OE1" <-> "OE2" Residue "A PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "B TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 256": "OE1" <-> "OE2" Residue "C TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17538 Number of models: 1 Model: "" Number of chains: 7 Chain: "1" Number of atoms: 7536 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 961, 7528 Classifications: {'peptide': 961} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 44, 'TRANS': 916} Chain breaks: 13 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 1, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 128 Conformer: "B" Number of residues, atoms: 961, 7528 Classifications: {'peptide': 961} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 44, 'TRANS': 916} Chain breaks: 13 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 1, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 128 bond proxies already assigned to first conformer: 7649 Chain: "A" Number of atoms: 2713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2713 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 316} Chain breaks: 4 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 3532 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 428, 3509 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 13, 'TRANS': 414} Chain breaks: 5 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 39 Conformer: "B" Number of residues, atoms: 428, 3509 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 13, 'TRANS': 414} Chain breaks: 5 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 39 bond proxies already assigned to first conformer: 3559 Chain: "C" Number of atoms: 3308 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 3294 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 5, 'PTRANS': 24, 'TRANS': 396} Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 8, 'ASN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 63 Conformer: "B" Number of residues, atoms: 426, 3294 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 5, 'PTRANS': 24, 'TRANS': 396} Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 8, 'ASN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 63 bond proxies already assigned to first conformer: 3355 Chain: "T" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 220 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "P" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 221 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna3p': 9} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12474 SG CYS B 336 80.144 94.688 100.636 1.00158.95 S ATOM 13241 SG CYS B 434 85.313 90.717 99.433 1.00138.98 S ATOM 13113 SG CYS B 417 81.693 88.069 98.997 1.00123.59 S ATOM 13559 SG CYS B 474 82.138 90.534 104.905 1.00120.32 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ACYS C 399 " occ=0.34 ... (10 atoms not shown) pdb=" SG BCYS C 399 " occ=0.66 Time building chain proxies: 15.36, per 1000 atoms: 0.88 Number of scatterers: 17538 At special positions: 0 Unit cell: (133.308, 148.212, 187.128, 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) Fe 4 26.01 S 95 16.00 P 21 15.00 O 3347 8.00 N 2971 7.00 C 11100 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: 6.40 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B 601 " pdb="FE2 SF4 B 601 " - pdb=" SG CYS B 434 " pdb="FE4 SF4 B 601 " - pdb=" SG CYS B 474 " pdb="FE3 SF4 B 601 " - pdb=" SG CYS B 417 " pdb="FE1 SF4 B 601 " - pdb=" SG CYS B 336 " Number of angles added : 12 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4146 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 14 sheets defined 43.6% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.58 Creating SS restraints... Processing helix chain '1' and resid 403 through 418 Proline residue: 1 412 - end of helix Processing helix chain '1' and resid 481 through 489 Processing helix chain '1' and resid 522 through 524 No H-bonds generated for 'chain '1' and resid 522 through 524' Processing helix chain '1' and resid 616 through 630 Processing helix chain '1' and resid 644 through 654 Processing helix chain '1' and resid 660 through 663 removed outlier: 3.571A pdb=" N ILE 1 663 " --> pdb=" O PHE 1 660 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 660 through 663' Processing helix chain '1' and resid 682 through 690 Processing helix chain '1' and resid 702 through 707 removed outlier: 3.540A pdb=" N LEU 1 707 " --> pdb=" O MET 1 703 " (cutoff:3.500A) Processing helix chain '1' and resid 716 through 724 Processing helix chain '1' and resid 738 through 741 Processing helix chain '1' and resid 744 through 768 Processing helix chain '1' and resid 770 through 781 Processing helix chain '1' and resid 785 through 790 Processing helix chain '1' and resid 799 through 807 Processing helix chain '1' and resid 868 through 876 Processing helix chain '1' and resid 905 through 926 removed outlier: 3.679A pdb=" N THR 1 926 " --> pdb=" O LYS 1 922 " (cutoff:3.500A) Processing helix chain '1' and resid 930 through 948 Processing helix chain '1' and resid 951 through 953 No H-bonds generated for 'chain '1' and resid 951 through 953' Processing helix chain '1' and resid 964 through 987 Processing helix chain '1' and resid 1009 through 1026 Processing helix chain '1' and resid 1072 through 1074 No H-bonds generated for 'chain '1' and resid 1072 through 1074' Processing helix chain '1' and resid 1080 through 1092 Processing helix chain '1' and resid 1101 through 1119 Processing helix chain '1' and resid 1124 through 1127 Processing helix chain '1' and resid 1147 through 1158 Processing helix chain '1' and resid 1196 through 1200 Processing helix chain '1' and resid 1202 through 1204 No H-bonds generated for 'chain '1' and resid 1202 through 1204' Processing helix chain '1' and resid 1210 through 1216 Processing helix chain '1' and resid 1219 through 1225 Processing helix chain '1' and resid 1234 through 1239 Processing helix chain '1' and resid 1323 through 1343 removed outlier: 4.547A pdb=" N GLN 11329 " --> pdb=" O GLN 11325 " (cutoff:3.500A) Processing helix chain '1' and resid 1382 through 1396 Processing helix chain '1' and resid 1398 through 1403 Processing helix chain '1' and resid 1424 through 1433 Processing helix chain '1' and resid 1435 through 1449 removed outlier: 4.199A pdb=" N TYR 11448 " --> pdb=" O VAL 11444 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 33 Processing helix chain 'A' and resid 40 through 43 No H-bonds generated for 'chain 'A' and resid 40 through 43' Processing helix chain 'A' and resid 65 through 75 Processing helix chain 'A' and resid 114 through 120 removed outlier: 5.378A pdb=" N ALA A 119 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 150 removed outlier: 4.774A pdb=" N PHE A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE A 137 " --> pdb=" O CYS A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 177 No H-bonds generated for 'chain 'A' and resid 174 through 177' Processing helix chain 'A' and resid 181 through 191 Processing helix chain 'A' and resid 211 through 228 Proline residue: A 222 - end of helix removed outlier: 3.911A pdb=" N VAL A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 244 Processing helix chain 'A' and resid 252 through 260 Processing helix chain 'A' and resid 271 through 284 removed outlier: 3.778A pdb=" N ASP A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 309 removed outlier: 4.187A pdb=" N ASP A 291 " --> pdb=" O PRO A 288 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER A 292 " --> pdb=" O LYS A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 372 through 392 Processing helix chain 'B' and resid 44 through 54 Processing helix chain 'B' and resid 72 through 94 Processing helix chain 'B' and resid 99 through 112 Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 121 through 140 removed outlier: 3.677A pdb=" N CYS B 139 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ARG B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 162 Processing helix chain 'B' and resid 165 through 173 Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 192 through 206 removed outlier: 4.648A pdb=" N ALA B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N SER B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 221 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 255 through 281 Proline residue: B 279 - end of helix Processing helix chain 'B' and resid 288 through 298 removed outlier: 4.044A pdb=" N TYR B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 325 No H-bonds generated for 'chain 'B' and resid 323 through 325' Processing helix chain 'B' and resid 327 through 332 removed outlier: 5.279A pdb=" N ASN B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 347 Processing helix chain 'B' and resid 352 through 365 Processing helix chain 'B' and resid 369 through 379 Processing helix chain 'B' and resid 388 through 394 Processing helix chain 'B' and resid 396 through 402 Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 435 through 438 No H-bonds generated for 'chain 'B' and resid 435 through 438' Processing helix chain 'B' and resid 441 through 451 Processing helix chain 'B' and resid 455 through 466 Processing helix chain 'B' and resid 470 through 481 Processing helix chain 'B' and resid 500 through 511 removed outlier: 3.614A pdb=" N GLN B 511 " --> pdb=" O SER B 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 275 Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 322 through 325 No H-bonds generated for 'chain 'C' and resid 322 through 325' Processing helix chain 'C' and resid 378 through 388 Processing helix chain 'C' and resid 411 through 422 Processing helix chain 'C' and resid 441 through 444 No H-bonds generated for 'chain 'C' and resid 441 through 444' Processing helix chain 'C' and resid 461 through 475 removed outlier: 3.852A pdb=" N THR C 470 " --> pdb=" O LEU C 466 " (cutoff:3.500A) Proline residue: C 471 - end of helix removed outlier: 3.905A pdb=" N THR C 475 " --> pdb=" O PRO C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 508 No H-bonds generated for 'chain 'C' and resid 505 through 508' Processing helix chain 'C' and resid 538 through 541 No H-bonds generated for 'chain 'C' and resid 538 through 541' Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 556 through 567 Processing helix chain 'C' and resid 614 through 620 removed outlier: 5.210A pdb=" N GLY C 618 " --> pdb=" O SER C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 625 No H-bonds generated for 'chain 'C' and resid 623 through 625' Processing sheet with id= A, first strand: chain '1' and resid 525 through 527 removed outlier: 3.549A pdb=" N MET 1 354 " --> pdb=" O LEU 1 497 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE 1 369 " --> pdb=" O LEU 1 357 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TYR 1 359 " --> pdb=" O ILE 1 367 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE 1 367 " --> pdb=" O TYR 1 359 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLU 1 361 " --> pdb=" O THR 1 365 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR 1 365 " --> pdb=" O GLU 1 361 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL 1 515 " --> pdb=" O MET 1 383 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N GLN 1 385 " --> pdb=" O VAL 1 515 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL 1 517 " --> pdb=" O GLN 1 385 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '1' and resid 424 through 431 removed outlier: 4.623A pdb=" N ARG 1 424 " --> pdb=" O LEU 1 449 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET 1 430 " --> pdb=" O SER 1 443 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER 1 443 " --> pdb=" O MET 1 430 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASP 1 444 " --> pdb=" O PRO 1 397 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU 1 446 " --> pdb=" O PHE 1 395 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE 1 395 " --> pdb=" O LEU 1 446 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N HIS 1 473 " --> pdb=" O LEU 1 396 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '1' and resid 695 through 698 removed outlier: 3.622A pdb=" N SER 1 562 " --> pdb=" O SER 1 540 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER 1 542 " --> pdb=" O THR 1 560 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER 1 558 " --> pdb=" O GLN 1 544 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU 1 546 " --> pdb=" O ILE 1 556 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ILE 1 556 " --> pdb=" O LEU 1 546 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ASN 1 548 " --> pdb=" O GLN 1 554 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN 1 554 " --> pdb=" O ASN 1 548 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N VAL 1 557 " --> pdb=" O ARG 1 587 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA 1 563 " --> pdb=" O ASP 1 581 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP 1 581 " --> pdb=" O ALA 1 563 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '1' and resid 854 through 856 removed outlier: 3.968A pdb=" N LEU 11041 " --> pdb=" O HIS 1 856 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '1' and resid 1033 through 1038 removed outlier: 4.265A pdb=" N ASP 11033 " --> pdb=" O ASP 1 864 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL 1 862 " --> pdb=" O ASP 11035 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL 11037 " --> pdb=" O VAL 1 860 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL 1 860 " --> pdb=" O VAL 11037 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR 1 994 " --> pdb=" O MET 11001 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP 11003 " --> pdb=" O VAL 1 992 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL 1 992 " --> pdb=" O ASP 11003 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '1' and resid 1129 through 1132 removed outlier: 3.694A pdb=" N ILE 11168 " --> pdb=" O MET 11131 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '1' and resid 1284 through 1286 Processing sheet with id= H, first strand: chain '1' and resid 1305 through 1307 Processing sheet with id= I, first strand: chain 'A' and resid 108 through 112 Processing sheet with id= J, first strand: chain 'B' and resid 225 through 228 removed outlier: 3.639A pdb=" N PHE B 242 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 316 through 319 removed outlier: 3.701A pdb=" N GLY C 352 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY C 298 " --> pdb=" O VAL C 348 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA C 349 " --> pdb=" O LEU C 366 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LYS C 353 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL C 362 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ARG C 331 " --> pdb=" O PHE C 360 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL C 362 " --> pdb=" O ARG C 331 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ASP C 333 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N SER C 364 " --> pdb=" O ASP C 333 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 340 through 342 Processing sheet with id= M, first strand: chain 'C' and resid 515 through 518 removed outlier: 6.615A pdb=" N THR C 482 " --> pdb=" O LYS C 516 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N MET C 518 " --> pdb=" O THR C 482 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU C 484 " --> pdb=" O MET C 518 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET C 431 " --> pdb=" O VAL C 483 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 522 through 526 removed outlier: 6.382A pdb=" N ILE C 630 " --> pdb=" O GLY C 532 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N SER C 534 " --> pdb=" O ILE C 630 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE C 632 " --> pdb=" O SER C 534 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL C 648 " --> pdb=" O MET C 631 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE C 633 " --> pdb=" O VAL C 648 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE C 650 " --> pdb=" O ILE C 633 " (cutoff:3.500A) 703 hydrogen bonds defined for protein. 1970 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: 5.33 Time building geometry restraints manager: 7.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.11: 1 1.11 - 1.41: 7290 1.41 - 1.70: 10516 1.70 - 1.99: 132 1.99 - 2.29: 13 Bond restraints: 17952 Sorted by residual: bond pdb=" CG PRO C 471 " pdb=" CD PRO C 471 " ideal model delta sigma weight residual 1.503 0.821 0.682 3.40e-02 8.65e+02 4.02e+02 bond pdb=" CB PRO C 471 " pdb=" CG PRO C 471 " ideal model delta sigma weight residual 1.492 2.276 -0.784 5.00e-02 4.00e+02 2.46e+02 bond pdb=" CA PRO C 471 " pdb=" CB PRO C 471 " ideal model delta sigma weight residual 1.533 1.421 0.113 1.42e-02 4.96e+03 6.28e+01 bond pdb=" N PRO C 471 " pdb=" CA PRO C 471 " ideal model delta sigma weight residual 1.469 1.554 -0.085 1.28e-02 6.10e+03 4.45e+01 bond pdb=" CA THR C 306 " pdb=" CB THR C 306 " ideal model delta sigma weight residual 1.525 1.582 -0.057 1.47e-02 4.63e+03 1.50e+01 ... (remaining 17947 not shown) Histogram of bond angle deviations from ideal: 51.14 - 67.96: 2 67.96 - 84.78: 13 84.78 - 101.60: 66 101.60 - 118.42: 14063 118.42 - 135.24: 10270 Bond angle restraints: 24414 Sorted by residual: angle pdb=" N PRO C 471 " pdb=" CD PRO C 471 " pdb=" CG PRO C 471 " ideal model delta sigma weight residual 103.20 51.14 52.06 1.50e+00 4.44e-01 1.20e+03 angle pdb=" CA PRO C 471 " pdb=" CB PRO C 471 " pdb=" CG PRO C 471 " ideal model delta sigma weight residual 104.50 51.66 52.84 1.90e+00 2.77e-01 7.73e+02 angle pdb=" N PRO C 471 " pdb=" CA PRO C 471 " pdb=" CB PRO C 471 " ideal model delta sigma weight residual 103.25 86.06 17.19 1.05e+00 9.07e-01 2.68e+02 angle pdb=" CA PRO C 471 " pdb=" N PRO C 471 " pdb=" CD PRO C 471 " ideal model delta sigma weight residual 112.00 92.13 19.87 1.40e+00 5.10e-01 2.02e+02 angle pdb=" CB PRO C 471 " pdb=" CG PRO C 471 " pdb=" CD PRO C 471 " ideal model delta sigma weight residual 106.10 68.87 37.23 3.20e+00 9.77e-02 1.35e+02 ... (remaining 24409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.14: 10536 28.14 - 56.28: 297 56.28 - 84.42: 41 84.42 - 112.57: 8 112.57 - 140.71: 1 Dihedral angle restraints: 10883 sinusoidal: 4512 harmonic: 6371 Sorted by residual: dihedral pdb=" CA PRO C 471 " pdb=" CB PRO C 471 " pdb=" CG PRO C 471 " pdb=" CD PRO C 471 " ideal model delta sinusoidal sigma weight residual -38.00 -178.71 140.71 1 2.00e+01 2.50e-03 4.26e+01 dihedral pdb=" N PRO C 471 " pdb=" C PRO C 471 " pdb=" CA PRO C 471 " pdb=" CB PRO C 471 " ideal model delta harmonic sigma weight residual 115.10 99.06 16.04 0 2.50e+00 1.60e-01 4.12e+01 dihedral pdb=" CA PHE C 350 " pdb=" C PHE C 350 " pdb=" N LYS C 351 " pdb=" CA LYS C 351 " ideal model delta harmonic sigma weight residual 180.00 155.10 24.90 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 10880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2305 0.056 - 0.111: 408 0.111 - 0.167: 34 0.167 - 0.223: 0 0.223 - 0.278: 3 Chirality restraints: 2750 Sorted by residual: chirality pdb=" CB ILE C 633 " pdb=" CA ILE C 633 " pdb=" CG1 ILE C 633 " pdb=" CG2 ILE C 633 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CB ILE 1 696 " pdb=" CA ILE 1 696 " pdb=" CG1 ILE 1 696 " pdb=" CG2 ILE 1 696 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE C 504 " pdb=" CA ILE C 504 " pdb=" CG1 ILE C 504 " pdb=" CG2 ILE C 504 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 2747 not shown) Planarity restraints: 3071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 470 " -0.090 5.00e-02 4.00e+02 1.21e-01 2.33e+01 pdb=" N PRO C 471 " 0.208 5.00e-02 4.00e+02 pdb=" CA PRO C 471 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 471 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP 1 671 " -0.081 5.00e-02 4.00e+02 1.16e-01 2.16e+01 pdb=" N PRO 1 672 " 0.200 5.00e-02 4.00e+02 pdb=" CA PRO 1 672 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO 1 672 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP 1 929 " 0.066 5.00e-02 4.00e+02 9.78e-02 1.53e+01 pdb=" N PRO 1 930 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO 1 930 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO 1 930 " 0.053 5.00e-02 4.00e+02 ... (remaining 3068 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 372 2.69 - 3.24: 17628 3.24 - 3.79: 27661 3.79 - 4.35: 36646 4.35 - 4.90: 58433 Nonbonded interactions: 140740 Sorted by model distance: nonbonded pdb=" O VAL A 191 " pdb=" OH TYR A 310 " model vdw 2.138 2.440 nonbonded pdb=" C THR C 470 " pdb=" CG PRO C 471 " model vdw 2.149 2.936 nonbonded pdb=" O CYS 1 953 " pdb=" OG SER 1 959 " model vdw 2.168 2.440 nonbonded pdb=" OG1 THR A 122 " pdb=" O GLN A 232 " model vdw 2.208 2.440 nonbonded pdb=" OG SER 1 433 " pdb=" O PHE 1 880 " model vdw 2.221 2.440 ... (remaining 140735 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.470 Check model and map are aligned: 0.230 Set scattering table: 0.160 Process input model: 57.060 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.090 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: 0.000 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: 66.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6204 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 : 0.009 0.784 17952 Z= 0.636 Angle : 0.901 52.835 24414 Z= 0.517 Chirality : 0.042 0.278 2750 Planarity : 0.006 0.121 3071 Dihedral : 13.630 140.708 6737 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.05 % Allowed : 0.27 % Favored : 99.68 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.71 % 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: 0.08 (0.18), residues: 2109 helix: 0.67 (0.17), residues: 969 sheet: -0.47 (0.32), residues: 244 loop : -0.34 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.003 TRP 1 785 HIS 0.009 0.001 HIS 11316 PHE 0.026 0.002 PHE B 75 TYR 0.018 0.002 TYR C 295 ARG 0.008 0.001 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 230 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 415 MET cc_start: 0.6252 (mtp) cc_final: 0.5869 (mtp) REVERT: 1 430 MET cc_start: 0.8137 (mtt) cc_final: 0.7654 (mtp) REVERT: 1 445 TYR cc_start: 0.4439 (m-80) cc_final: 0.3989 (m-80) REVERT: 1 619 MET cc_start: 0.6364 (ttt) cc_final: 0.6050 (ttt) REVERT: 1 929 ASP cc_start: 0.8501 (m-30) cc_final: 0.8289 (m-30) REVERT: 1 1237 LEU cc_start: 0.4921 (tp) cc_final: 0.4072 (tp) REVERT: 1 1341 TYR cc_start: 0.7363 (t80) cc_final: 0.6561 (t80) REVERT: 1 1351 SER cc_start: 0.9179 (m) cc_final: 0.8894 (t) REVERT: 1 1376 MET cc_start: 0.7844 (tpp) cc_final: 0.7488 (tpp) REVERT: 1 1392 PHE cc_start: 0.7054 (m-10) cc_final: 0.6852 (m-10) REVERT: 1 1404 GLN cc_start: 0.6866 (mt0) cc_final: 0.6455 (mt0) REVERT: A 141 MET cc_start: 0.5944 (mtm) cc_final: 0.5629 (mtm) REVERT: A 158 ILE cc_start: 0.7786 (pt) cc_final: 0.7479 (mm) REVERT: A 274 TRP cc_start: 0.7669 (t-100) cc_final: 0.7299 (t-100) REVERT: B 83 LEU cc_start: 0.6785 (tp) cc_final: 0.6428 (tp) REVERT: B 157 LYS cc_start: 0.8337 (mttt) cc_final: 0.7923 (mtpp) REVERT: B 243 LEU cc_start: 0.6798 (mp) cc_final: 0.6509 (mm) REVERT: B 275 TYR cc_start: 0.6404 (t80) cc_final: 0.5579 (t80) REVERT: B 430 ASP cc_start: 0.5472 (m-30) cc_final: 0.5043 (m-30) REVERT: C 259 ASP cc_start: 0.7050 (m-30) cc_final: 0.6750 (m-30) REVERT: C 281 ASN cc_start: 0.8139 (m-40) cc_final: 0.7873 (t0) REVERT: C 463 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7386 (tt0) REVERT: C 613 ASP cc_start: 0.6444 (t0) cc_final: 0.6232 (t0) REVERT: C 630 ILE cc_start: 0.8599 (mt) cc_final: 0.8374 (mt) outliers start: 1 outliers final: 1 residues processed: 231 average time/residue: 0.3110 time to fit residues: 107.3892 Evaluate side-chains 141 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 168 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 125 optimal weight: 20.0000 chunk 195 optimal weight: 2.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 407 HIS 1 524 ASN 1 653 HIS 11359 GLN A 60 ASN A 168 HIS A 275 ASN B 332 ASN ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6280 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 17952 Z= 0.372 Angle : 0.767 12.646 24414 Z= 0.394 Chirality : 0.048 0.239 2750 Planarity : 0.007 0.074 3071 Dihedral : 8.293 73.678 2579 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.11 % Allowed : 3.68 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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 (0.18), residues: 2109 helix: 0.30 (0.16), residues: 961 sheet: -0.76 (0.30), residues: 254 loop : -0.70 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP B 78 HIS 0.010 0.002 HIS B 131 PHE 0.035 0.003 PHE B 75 TYR 0.032 0.003 TYR B 275 ARG 0.009 0.001 ARG 1 669 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 430 MET cc_start: 0.7858 (mtt) cc_final: 0.7456 (mtp) REVERT: 1 633 ASP cc_start: 0.6582 (m-30) cc_final: 0.6242 (t0) REVERT: 1 703 MET cc_start: 0.7141 (tpp) cc_final: 0.6878 (tpp) REVERT: 1 1237 LEU cc_start: 0.4964 (tp) cc_final: 0.4157 (tp) REVERT: 1 1351 SER cc_start: 0.9197 (m) cc_final: 0.8938 (t) REVERT: 1 1376 MET cc_start: 0.7956 (tpp) cc_final: 0.7488 (tpp) REVERT: A 158 ILE cc_start: 0.7721 (pt) cc_final: 0.7439 (mm) REVERT: A 274 TRP cc_start: 0.7618 (t-100) cc_final: 0.7183 (t-100) REVERT: B 157 LYS cc_start: 0.8368 (mttt) cc_final: 0.7966 (tptm) REVERT: B 243 LEU cc_start: 0.6873 (mp) cc_final: 0.6566 (mm) REVERT: B 470 TYR cc_start: 0.3279 (m-10) cc_final: 0.3012 (m-10) REVERT: C 281 ASN cc_start: 0.8318 (m-40) cc_final: 0.7861 (t0) REVERT: C 613 ASP cc_start: 0.6425 (t0) cc_final: 0.6215 (t0) outliers start: 1 outliers final: 0 residues processed: 166 average time/residue: 0.2811 time to fit residues: 73.5140 Evaluate side-chains 127 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 108 optimal weight: 0.1980 chunk 60 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 195 optimal weight: 7.9990 chunk 211 optimal weight: 10.0000 chunk 174 optimal weight: 20.0000 chunk 193 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 overall best weight: 5.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11055 ASN A 71 GLN A 275 ASN ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 693 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6270 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 17952 Z= 0.316 Angle : 0.687 11.964 24414 Z= 0.352 Chirality : 0.045 0.191 2750 Planarity : 0.005 0.081 3071 Dihedral : 8.332 73.705 2579 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.05 % Allowed : 3.41 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.56 (0.18), residues: 2109 helix: 0.32 (0.16), residues: 951 sheet: -0.85 (0.31), residues: 243 loop : -0.87 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 78 HIS 0.007 0.002 HIS A 240 PHE 0.030 0.003 PHE B 75 TYR 0.028 0.002 TYR B 333 ARG 0.006 0.001 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 2.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 547 MET cc_start: 0.6048 (ptp) cc_final: 0.5805 (ptp) REVERT: 1 614 ASN cc_start: 0.6620 (p0) cc_final: 0.6367 (p0) REVERT: 1 633 ASP cc_start: 0.6428 (m-30) cc_final: 0.5984 (t0) REVERT: 1 703 MET cc_start: 0.7031 (tpp) cc_final: 0.6811 (tpp) REVERT: 1 1237 LEU cc_start: 0.5075 (tp) cc_final: 0.4113 (tp) REVERT: 1 1351 SER cc_start: 0.9158 (m) cc_final: 0.8893 (t) REVERT: 1 1376 MET cc_start: 0.7995 (tpp) cc_final: 0.7591 (tpp) REVERT: B 83 LEU cc_start: 0.6441 (tp) cc_final: 0.6176 (tt) REVERT: B 157 LYS cc_start: 0.8224 (mttt) cc_final: 0.7812 (mtpt) REVERT: B 441 HIS cc_start: 0.6222 (m170) cc_final: 0.5975 (m-70) REVERT: B 470 TYR cc_start: 0.3505 (m-10) cc_final: 0.3284 (m-10) REVERT: C 281 ASN cc_start: 0.8272 (m-40) cc_final: 0.8014 (m-40) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2952 time to fit residues: 72.3987 Evaluate side-chains 122 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 193 optimal weight: 7.9990 chunk 147 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 131 optimal weight: 0.9980 chunk 196 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 chunk 186 optimal weight: 6.9990 chunk 56 optimal weight: 0.0020 overall best weight: 1.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 ASN C 346 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6203 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17952 Z= 0.173 Angle : 0.560 12.414 24414 Z= 0.283 Chirality : 0.041 0.231 2750 Planarity : 0.004 0.064 3071 Dihedral : 7.914 73.609 2579 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.05 % Allowed : 1.86 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.00 (0.18), residues: 2109 helix: 0.87 (0.17), residues: 977 sheet: -0.68 (0.30), residues: 261 loop : -0.69 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 376 HIS 0.004 0.001 HIS 1 728 PHE 0.023 0.002 PHE B 75 TYR 0.014 0.001 TYR B 275 ARG 0.007 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 614 ASN cc_start: 0.6680 (p0) cc_final: 0.6478 (p0) REVERT: 1 619 MET cc_start: 0.6375 (ttt) cc_final: 0.6149 (ttt) REVERT: 1 633 ASP cc_start: 0.6348 (m-30) cc_final: 0.5963 (t0) REVERT: 1 703 MET cc_start: 0.7057 (tpp) cc_final: 0.6841 (tpp) REVERT: 1 1351 SER cc_start: 0.9103 (m) cc_final: 0.8824 (t) REVERT: 1 1376 MET cc_start: 0.7927 (tpp) cc_final: 0.7567 (tpp) REVERT: A 114 MET cc_start: 0.6653 (mmt) cc_final: 0.6295 (mmm) REVERT: A 158 ILE cc_start: 0.7713 (pt) cc_final: 0.7438 (mm) REVERT: B 116 PHE cc_start: 0.6572 (p90) cc_final: 0.6255 (p90) REVERT: B 157 LYS cc_start: 0.8270 (mttt) cc_final: 0.7764 (mtpt) REVERT: B 243 LEU cc_start: 0.6436 (mt) cc_final: 0.6224 (mm) REVERT: B 470 TYR cc_start: 0.3179 (m-10) cc_final: 0.2899 (m-10) REVERT: C 281 ASN cc_start: 0.8207 (m-40) cc_final: 0.7701 (t0) REVERT: C 378 SER cc_start: 0.8719 (p) cc_final: 0.7953 (t) REVERT: C 613 ASP cc_start: 0.6459 (t70) cc_final: 0.6253 (t0) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2772 time to fit residues: 72.6804 Evaluate side-chains 127 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 173 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 154 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 177 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 106 optimal weight: 8.9990 chunk 186 optimal weight: 9.9990 chunk 52 optimal weight: 0.0000 overall best weight: 3.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6228 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17952 Z= 0.228 Angle : 0.587 10.320 24414 Z= 0.297 Chirality : 0.042 0.221 2750 Planarity : 0.005 0.062 3071 Dihedral : 7.992 73.502 2579 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.11 % Allowed : 1.81 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.18), residues: 2109 helix: 0.86 (0.17), residues: 974 sheet: -0.66 (0.31), residues: 243 loop : -0.73 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 274 HIS 0.005 0.001 HIS B 499 PHE 0.023 0.002 PHE B 75 TYR 0.020 0.002 TYR B 275 ARG 0.011 0.001 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 2.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 547 MET cc_start: 0.6120 (ptp) cc_final: 0.5882 (ptp) REVERT: 1 633 ASP cc_start: 0.6413 (m-30) cc_final: 0.5971 (t0) REVERT: 1 703 MET cc_start: 0.7052 (tpp) cc_final: 0.6811 (tpp) REVERT: 1 1351 SER cc_start: 0.9109 (m) cc_final: 0.8833 (t) REVERT: 1 1376 MET cc_start: 0.7929 (tpp) cc_final: 0.7466 (tpp) REVERT: A 114 MET cc_start: 0.6803 (mmt) cc_final: 0.6459 (mmm) REVERT: B 83 LEU cc_start: 0.6469 (tp) cc_final: 0.6268 (tp) REVERT: B 157 LYS cc_start: 0.8298 (mttt) cc_final: 0.7848 (tptt) REVERT: B 470 TYR cc_start: 0.3158 (m-10) cc_final: 0.2924 (m-10) REVERT: C 281 ASN cc_start: 0.8246 (m-40) cc_final: 0.7772 (t0) REVERT: C 378 SER cc_start: 0.8720 (p) cc_final: 0.7937 (t) REVERT: C 450 ASN cc_start: 0.8205 (t0) cc_final: 0.7583 (p0) REVERT: C 613 ASP cc_start: 0.6502 (t70) cc_final: 0.6149 (t0) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.2994 time to fit residues: 70.7282 Evaluate side-chains 125 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 69 optimal weight: 9.9990 chunk 187 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 208 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 752 GLN 11055 ASN A 71 GLN B 401 HIS C 346 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17952 Z= 0.264 Angle : 0.642 10.752 24414 Z= 0.324 Chirality : 0.044 0.218 2750 Planarity : 0.005 0.059 3071 Dihedral : 8.238 73.581 2579 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.11 % Allowed : 1.17 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.24 (0.18), residues: 2109 helix: 0.67 (0.17), residues: 961 sheet: -0.75 (0.33), residues: 222 loop : -0.81 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 376 HIS 0.009 0.001 HIS A 240 PHE 0.024 0.002 PHE B 75 TYR 0.023 0.002 TYR 11378 ARG 0.005 0.001 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 547 MET cc_start: 0.5967 (ptp) cc_final: 0.5723 (ptp) REVERT: 1 619 MET cc_start: 0.6404 (ttt) cc_final: 0.6109 (ttt) REVERT: 1 633 ASP cc_start: 0.6336 (m-30) cc_final: 0.5880 (t0) REVERT: 1 703 MET cc_start: 0.6941 (tpp) cc_final: 0.6663 (tpp) REVERT: 1 1351 SER cc_start: 0.9125 (m) cc_final: 0.8836 (t) REVERT: 1 1376 MET cc_start: 0.7997 (tpp) cc_final: 0.7407 (tpp) REVERT: 1 1380 TYR cc_start: 0.6928 (t80) cc_final: 0.6708 (t80) REVERT: B 83 LEU cc_start: 0.6539 (tp) cc_final: 0.6211 (tt) REVERT: B 157 LYS cc_start: 0.8274 (mttt) cc_final: 0.7763 (tptm) REVERT: B 470 TYR cc_start: 0.3323 (m-10) cc_final: 0.3067 (m-10) REVERT: C 281 ASN cc_start: 0.8257 (m-40) cc_final: 0.8031 (m-40) REVERT: C 378 SER cc_start: 0.8651 (p) cc_final: 0.7853 (t) REVERT: C 613 ASP cc_start: 0.6589 (t70) cc_final: 0.6337 (t0) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.2702 time to fit residues: 67.5951 Evaluate side-chains 124 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 200 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 151 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 175 optimal weight: 0.0030 chunk 116 optimal weight: 0.1980 chunk 207 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 chunk 126 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 712 GLN ** 11433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 ASN C 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6194 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17952 Z= 0.164 Angle : 0.537 9.417 24414 Z= 0.271 Chirality : 0.041 0.208 2750 Planarity : 0.004 0.058 3071 Dihedral : 7.881 73.608 2579 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.11 % Allowed : 0.80 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.12 (0.18), residues: 2109 helix: 1.04 (0.17), residues: 972 sheet: -0.60 (0.33), residues: 222 loop : -0.72 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 376 HIS 0.004 0.001 HIS 1 728 PHE 0.025 0.002 PHE 1 352 TYR 0.013 0.001 TYR 1 359 ARG 0.003 0.000 ARG B 409 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 547 MET cc_start: 0.5960 (ptp) cc_final: 0.5685 (ptp) REVERT: 1 619 MET cc_start: 0.6417 (ttt) cc_final: 0.6127 (ttt) REVERT: 1 633 ASP cc_start: 0.6292 (m-30) cc_final: 0.5876 (t0) REVERT: 1 703 MET cc_start: 0.6997 (tpp) cc_final: 0.6759 (tpp) REVERT: 1 1351 SER cc_start: 0.9089 (m) cc_final: 0.8800 (t) REVERT: 1 1376 MET cc_start: 0.7919 (tpp) cc_final: 0.7450 (tpp) REVERT: A 20 LYS cc_start: 0.7898 (tptp) cc_final: 0.7677 (tppt) REVERT: A 71 GLN cc_start: 0.6325 (mt0) cc_final: 0.6090 (mt0) REVERT: A 114 MET cc_start: 0.6654 (mmt) cc_final: 0.6324 (mmm) REVERT: A 158 ILE cc_start: 0.7695 (pt) cc_final: 0.7342 (mm) REVERT: B 157 LYS cc_start: 0.8264 (mttt) cc_final: 0.7664 (tptm) REVERT: B 243 LEU cc_start: 0.6234 (mt) cc_final: 0.5977 (mm) REVERT: B 256 LEU cc_start: 0.6421 (tp) cc_final: 0.5925 (tp) REVERT: B 470 TYR cc_start: 0.3085 (m-10) cc_final: 0.2803 (m-10) REVERT: C 281 ASN cc_start: 0.8218 (m-40) cc_final: 0.7977 (m-40) REVERT: C 378 SER cc_start: 0.8665 (p) cc_final: 0.7918 (t) REVERT: C 613 ASP cc_start: 0.6438 (t70) cc_final: 0.6100 (t0) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.2636 time to fit residues: 66.7372 Evaluate side-chains 124 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 128 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 131 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 chunk 188 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11055 ASN ** 11433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN B 347 ASN B 441 HIS C 346 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17952 Z= 0.314 Angle : 0.673 11.684 24414 Z= 0.342 Chirality : 0.045 0.211 2750 Planarity : 0.005 0.058 3071 Dihedral : 8.342 73.625 2579 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.11 % Allowed : 1.07 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.18), residues: 2109 helix: 0.53 (0.17), residues: 951 sheet: -0.66 (0.34), residues: 214 loop : -0.87 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP B 376 HIS 0.007 0.002 HIS B 293 PHE 0.027 0.003 PHE B 61 TYR 0.027 0.002 TYR B 275 ARG 0.006 0.001 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 619 MET cc_start: 0.6454 (ttt) cc_final: 0.6122 (ttt) REVERT: 1 633 ASP cc_start: 0.6363 (m-30) cc_final: 0.5862 (t0) REVERT: 1 703 MET cc_start: 0.6990 (tpp) cc_final: 0.6724 (tpp) REVERT: 1 956 TYR cc_start: 0.6125 (m-80) cc_final: 0.5832 (m-80) REVERT: 1 1351 SER cc_start: 0.9123 (m) cc_final: 0.8823 (t) REVERT: 1 1376 MET cc_start: 0.7966 (tpp) cc_final: 0.7337 (tpp) REVERT: A 20 LYS cc_start: 0.7908 (tptp) cc_final: 0.7694 (tppt) REVERT: B 83 LEU cc_start: 0.6492 (tp) cc_final: 0.6203 (tt) REVERT: B 116 PHE cc_start: 0.6717 (p90) cc_final: 0.6467 (p90) REVERT: B 157 LYS cc_start: 0.8244 (mttt) cc_final: 0.7747 (tptm) REVERT: C 378 SER cc_start: 0.8641 (p) cc_final: 0.7851 (t) REVERT: C 613 ASP cc_start: 0.6630 (t70) cc_final: 0.6306 (t0) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2915 time to fit residues: 66.3560 Evaluate side-chains 121 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 198 optimal weight: 4.9990 chunk 181 optimal weight: 8.9990 chunk 193 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 151 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 174 optimal weight: 9.9990 chunk 182 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 chunk 126 optimal weight: 0.0060 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 681 ASN ** 11433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 ASN C 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6181 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 17952 Z= 0.154 Angle : 0.542 11.584 24414 Z= 0.270 Chirality : 0.041 0.218 2750 Planarity : 0.004 0.056 3071 Dihedral : 7.856 73.654 2579 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.11 % Allowed : 0.64 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.18), residues: 2109 helix: 1.05 (0.17), residues: 965 sheet: -0.53 (0.34), residues: 222 loop : -0.70 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 1 714 HIS 0.004 0.001 HIS B 499 PHE 0.023 0.002 PHE B 75 TYR 0.012 0.001 TYR B 275 ARG 0.006 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 2.115 Fit side-chains revert: symmetry clash REVERT: 1 415 MET cc_start: 0.7125 (mmm) cc_final: 0.6564 (mtp) REVERT: 1 619 MET cc_start: 0.6462 (ttt) cc_final: 0.6126 (ttt) REVERT: 1 633 ASP cc_start: 0.6204 (m-30) cc_final: 0.5793 (t0) REVERT: 1 703 MET cc_start: 0.7089 (tpp) cc_final: 0.6853 (tpp) REVERT: 1 956 TYR cc_start: 0.6281 (m-80) cc_final: 0.5996 (m-80) REVERT: 1 1351 SER cc_start: 0.9078 (m) cc_final: 0.8784 (t) REVERT: 1 1376 MET cc_start: 0.7890 (tpp) cc_final: 0.7413 (tpp) REVERT: A 20 LYS cc_start: 0.7857 (tptp) cc_final: 0.7609 (tppt) REVERT: A 114 MET cc_start: 0.6664 (mmt) cc_final: 0.6342 (mmm) REVERT: A 158 ILE cc_start: 0.7763 (pt) cc_final: 0.7427 (mm) REVERT: A 188 LEU cc_start: 0.5989 (tp) cc_final: 0.5597 (mt) REVERT: B 157 LYS cc_start: 0.8219 (mttt) cc_final: 0.7658 (tptm) REVERT: B 243 LEU cc_start: 0.6319 (mt) cc_final: 0.6061 (mm) REVERT: B 256 LEU cc_start: 0.6376 (tp) cc_final: 0.5843 (tp) REVERT: B 470 TYR cc_start: 0.3094 (m-10) cc_final: 0.2838 (m-10) REVERT: C 281 ASN cc_start: 0.8314 (m-40) cc_final: 0.8079 (m-40) REVERT: C 378 SER cc_start: 0.8640 (p) cc_final: 0.7931 (t) REVERT: C 613 ASP cc_start: 0.6405 (t70) cc_final: 0.6190 (t0) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.2827 time to fit residues: 68.4800 Evaluate side-chains 129 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 204 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 96 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 chunk 197 optimal weight: 6.9990 chunk 170 optimal weight: 0.0980 chunk 17 optimal weight: 0.0050 chunk 131 optimal weight: 6.9990 chunk 104 optimal weight: 0.3980 chunk 135 optimal weight: 0.4980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 11433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 ASN C 346 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6146 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17952 Z= 0.139 Angle : 0.528 10.667 24414 Z= 0.265 Chirality : 0.040 0.223 2750 Planarity : 0.004 0.057 3071 Dihedral : 7.561 73.535 2579 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.11 % Allowed : 0.53 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.41 (0.19), residues: 2109 helix: 1.33 (0.17), residues: 960 sheet: -0.53 (0.33), residues: 230 loop : -0.58 (0.21), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 376 HIS 0.006 0.001 HIS A 323 PHE 0.031 0.002 PHE A 62 TYR 0.012 0.001 TYR B 503 ARG 0.009 0.000 ARG 1 669 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 415 MET cc_start: 0.6987 (mmm) cc_final: 0.6439 (mtp) REVERT: 1 445 TYR cc_start: 0.4587 (m-80) cc_final: 0.4380 (m-80) REVERT: 1 619 MET cc_start: 0.6431 (ttt) cc_final: 0.6119 (ttt) REVERT: 1 633 ASP cc_start: 0.6183 (m-30) cc_final: 0.5820 (t0) REVERT: 1 703 MET cc_start: 0.7082 (tpp) cc_final: 0.6869 (tpp) REVERT: 1 956 TYR cc_start: 0.6265 (m-80) cc_final: 0.6010 (m-80) REVERT: 1 1351 SER cc_start: 0.9023 (m) cc_final: 0.8734 (t) REVERT: 1 1376 MET cc_start: 0.7825 (tpp) cc_final: 0.7324 (tpp) REVERT: A 114 MET cc_start: 0.6696 (mmt) cc_final: 0.6357 (mmm) REVERT: A 121 ARG cc_start: 0.5167 (pmt170) cc_final: 0.4374 (ptt-90) REVERT: A 158 ILE cc_start: 0.7833 (pt) cc_final: 0.7508 (mm) REVERT: B 83 LEU cc_start: 0.6124 (tp) cc_final: 0.5918 (tp) REVERT: B 157 LYS cc_start: 0.8272 (mttt) cc_final: 0.7742 (tptm) REVERT: B 160 PHE cc_start: 0.7453 (t80) cc_final: 0.6682 (t80) REVERT: B 243 LEU cc_start: 0.6330 (mt) cc_final: 0.6098 (mm) REVERT: B 256 LEU cc_start: 0.6324 (tp) cc_final: 0.5557 (tp) REVERT: C 281 ASN cc_start: 0.8319 (m-40) cc_final: 0.7841 (t0) REVERT: C 378 SER cc_start: 0.8646 (p) cc_final: 0.8005 (t) REVERT: C 613 ASP cc_start: 0.6436 (t70) cc_final: 0.6139 (t0) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2843 time to fit residues: 72.2442 Evaluate side-chains 125 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 9.9990 chunk 52 optimal weight: 0.0980 chunk 157 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 170 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 chunk 175 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.0470 chunk 149 optimal weight: 10.0000 overall best weight: 2.2284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 ASN C 346 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.060251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.049411 restraints weight = 339603.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.051125 restraints weight = 240719.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.052390 restraints weight = 141714.671| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17952 Z= 0.174 Angle : 0.535 8.990 24414 Z= 0.268 Chirality : 0.041 0.217 2750 Planarity : 0.004 0.057 3071 Dihedral : 7.659 73.486 2579 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.11 % Allowed : 0.37 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.19), residues: 2109 helix: 1.36 (0.17), residues: 955 sheet: -0.47 (0.34), residues: 229 loop : -0.63 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 376 HIS 0.007 0.001 HIS A 323 PHE 0.026 0.002 PHE A 62 TYR 0.037 0.001 TYR B 333 ARG 0.010 0.000 ARG 1 669 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3210.74 seconds wall clock time: 59 minutes 31.52 seconds (3571.52 seconds total)