Starting phenix.real_space_refine on Mon Nov 18 22:03:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foj_29351/11_2024/8foj_29351.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foj_29351/11_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_29351/11_2024/8foj_29351.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foj_29351/11_2024/8foj_29351.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foj_29351/11_2024/8foj_29351.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foj_29351/11_2024/8foj_29351.cif" } 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. Time to flip 31 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 16.67, per 1000 atoms: 0.95 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 - 3.00 Amino acid : True - 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: 4.55 Conformation dependent library (CDL) restraints added in 3.9 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... Secondary structure from input PDB file: 90 helices and 19 sheets defined 51.0% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain '1' and resid 402 through 419 Proline residue: 1 412 - end of helix Processing helix chain '1' and resid 480 through 489 Processing helix chain '1' and resid 521 through 523 No H-bonds generated for 'chain '1' and resid 521 through 523' Processing helix chain '1' and resid 615 through 631 removed outlier: 3.734A pdb=" N MET 1 619 " --> pdb=" O ASN 1 615 " (cutoff:3.500A) Processing helix chain '1' and resid 643 through 655 Processing helix chain '1' and resid 659 through 664 removed outlier: 3.571A pdb=" N ILE 1 663 " --> pdb=" O PHE 1 660 " (cutoff:3.500A) Processing helix chain '1' and resid 682 through 691 Processing helix chain '1' and resid 701 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 715 through 725 Processing helix chain '1' and resid 737 through 742 removed outlier: 3.666A pdb=" N ASN 1 742 " --> pdb=" O GLN 1 739 " (cutoff:3.500A) Processing helix chain '1' and resid 743 through 769 removed outlier: 3.629A pdb=" N MET 1 747 " --> pdb=" O ASP 1 743 " (cutoff:3.500A) Processing helix chain '1' and resid 769 through 782 Processing helix chain '1' and resid 784 through 791 Processing helix chain '1' and resid 798 through 807 Processing helix chain '1' and resid 867 through 877 Processing helix chain '1' and resid 904 through 927 removed outlier: 3.679A pdb=" N THR 1 926 " --> pdb=" O LYS 1 922 " (cutoff:3.500A) Processing helix chain '1' and resid 929 through 949 Processing helix chain '1' and resid 950 through 954 Processing helix chain '1' and resid 963 through 988 Processing helix chain '1' and resid 1008 through 1027 Processing helix chain '1' and resid 1071 through 1075 Processing helix chain '1' and resid 1079 through 1093 Processing helix chain '1' and resid 1101 through 1120 Processing helix chain '1' and resid 1123 through 1128 Processing helix chain '1' and resid 1146 through 1159 Processing helix chain '1' and resid 1196 through 1201 removed outlier: 3.619A pdb=" N ILE 11201 " --> pdb=" O ASN 11197 " (cutoff:3.500A) Processing helix chain '1' and resid 1202 through 1205 removed outlier: 3.687A pdb=" N ASN 11205 " --> pdb=" O LYS 11202 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 1202 through 1205' Processing helix chain '1' and resid 1209 through 1217 Processing helix chain '1' and resid 1218 through 1226 Processing helix chain '1' and resid 1233 through 1240 Processing helix chain '1' and resid 1322 through 1343 removed outlier: 4.547A pdb=" N GLN 11329 " --> pdb=" O GLN 11325 " (cutoff:3.500A) Processing helix chain '1' and resid 1381 through 1396 Processing helix chain '1' and resid 1397 through 1404 Processing helix chain '1' and resid 1423 through 1434 Processing helix chain '1' and resid 1434 through 1450 removed outlier: 4.199A pdb=" N TYR 11448 " --> pdb=" O VAL 11444 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 34 removed outlier: 3.684A pdb=" N HIS A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 113 through 121 removed outlier: 3.698A pdb=" N ASP A 116 " --> pdb=" O ASP A 113 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ALA A 119 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG A 121 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 151 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 173 through 178 removed outlier: 3.512A pdb=" N ALA A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 192 Processing helix chain 'A' and resid 210 through 229 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 237 through 245 Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 271 through 285 removed outlier: 3.778A pdb=" N ASP A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 310 removed outlier: 3.750A pdb=" N HIS A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 320 removed outlier: 4.079A pdb=" N LYS A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLN A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 through 320' Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 372 through 393 Processing helix chain 'B' and resid 43 through 55 Processing helix chain 'B' and resid 71 through 95 removed outlier: 3.527A pdb=" N ARG B 95 " --> pdb=" O SER B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 113 Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 120 through 139 removed outlier: 3.677A pdb=" N CYS B 139 " --> pdb=" O ARG B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 163 Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'B' and resid 184 through 191 Processing helix chain 'B' and resid 191 through 207 removed outlier: 3.668A pdb=" N LEU B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) 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 211 through 222 removed outlier: 3.605A pdb=" N ARG B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 231 Processing helix chain 'B' and resid 232 through 238 removed outlier: 3.759A pdb=" N ASN B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 282 Proline residue: B 279 - end of helix Processing helix chain 'B' and resid 287 through 297 Processing helix chain 'B' and resid 322 through 325 removed outlier: 3.553A pdb=" N TRP B 325 " --> pdb=" O GLN B 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 322 through 325' Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 334 through 348 Processing helix chain 'B' and resid 351 through 366 Processing helix chain 'B' and resid 368 through 380 removed outlier: 3.746A pdb=" N PHE B 380 " --> pdb=" O TRP B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 395 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'B' and resid 434 through 439 Processing helix chain 'B' and resid 440 through 451 Processing helix chain 'B' and resid 454 through 467 removed outlier: 3.512A pdb=" N LYS B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 482 removed outlier: 3.657A pdb=" N ALA B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 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 253 through 276 Processing helix chain 'C' and resid 279 through 283 Processing helix chain 'C' and resid 321 through 326 removed outlier: 3.528A pdb=" N GLY C 325 " --> pdb=" O SER C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 389 Processing helix chain 'C' and resid 410 through 423 Processing helix chain 'C' and resid 440 through 445 Processing helix chain 'C' and resid 460 through 474 removed outlier: 3.852A pdb=" N THR C 470 " --> pdb=" O LEU C 466 " (cutoff:3.500A) Proline residue: C 471 - end of helix Processing helix chain 'C' and resid 504 through 509 Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 548 through 554 removed outlier: 3.700A pdb=" N SER C 552 " --> pdb=" O GLY C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 568 Processing helix chain 'C' and resid 613 through 621 removed outlier: 5.210A pdb=" N GLY C 618 " --> pdb=" O SER C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 626 Processing helix chain 'C' and resid 693 through 697 removed outlier: 3.684A pdb=" N ARG C 697 " --> pdb=" O ASN C 693 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 693 through 697' Processing sheet with id=AA1, first strand: chain '1' and resid 515 through 519 removed outlier: 6.689A pdb=" N SER 1 381 " --> pdb=" O VAL 1 515 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N VAL 1 517 " --> pdb=" O SER 1 381 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N MET 1 383 " --> pdb=" O VAL 1 517 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL 1 519 " --> pdb=" O MET 1 383 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLN 1 385 " --> pdb=" O VAL 1 519 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR 1 365 " --> pdb=" O GLU 1 361 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLU 1 361 " --> pdb=" O THR 1 365 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE 1 367 " --> pdb=" O TYR 1 359 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TYR 1 359 " --> pdb=" O ILE 1 367 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE 1 369 " --> pdb=" O LEU 1 357 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET 1 354 " --> pdb=" O LEU 1 497 " (cutoff:3.500A) Processing sheet with id=AA2, 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: 6.354A pdb=" N PHE 1 394 " --> pdb=" O VAL 1 474 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL 1 474 " --> pdb=" O PHE 1 394 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU 1 396 " --> pdb=" O TYR 1 472 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 610 through 612 removed outlier: 7.817A pdb=" N ARG 1 611 " --> pdb=" O LEU 1 582 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR 1 584 " --> pdb=" O ARG 1 611 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS 1 553 " --> pdb=" O ASN 1 548 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N GLN 1 544 " --> pdb=" O VAL 1 557 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ILE 1 559 " --> pdb=" O SER 1 542 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N SER 1 542 " --> pdb=" O ILE 1 559 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU 1 561 " --> pdb=" O SER 1 540 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER 1 540 " --> pdb=" O LEU 1 561 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ALA 1 563 " --> pdb=" O CYS 1 538 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N CYS 1 538 " --> pdb=" O ALA 1 563 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU 1 539 " --> pdb=" O ILE 1 636 " (cutoff:3.500A) Processing sheet with id=AA4, 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) 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=AA5, 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) removed outlier: 5.969A pdb=" N PHE 11038 " --> pdb=" O VAL 11054 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL 11054 " --> pdb=" O PHE 11038 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS 11040 " --> pdb=" O LEU 11052 " (cutoff:3.500A) Processing sheet with id=AA6, 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=AA7, first strand: chain '1' and resid 1284 through 1286 Processing sheet with id=AA8, first strand: chain '1' and resid 1305 through 1307 Processing sheet with id=AA9, first strand: chain '1' and resid 1356 through 1357 Processing sheet with id=AB1, first strand: chain 'A' and resid 45 through 48 removed outlier: 4.578A pdb=" N GLU A 46 " --> pdb=" O GLY A 83 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 45 through 48 removed outlier: 4.578A pdb=" N GLU A 46 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 325 " --> pdb=" O ILE A 82 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 108 through 112 removed outlier: 4.457A pdb=" N TRP A 159 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 181 through 182 removed outlier: 4.091A pdb=" N GLN B 181 " --> pdb=" O LYS B 226 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 242 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 294 through 302 removed outlier: 5.033A pdb=" N LEU C 316 " --> pdb=" O LEU C 332 " (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) removed outlier: 5.587A pdb=" N VAL C 362 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LYS C 353 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA C 349 " --> pdb=" O LEU C 366 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY C 298 " --> pdb=" O VAL C 348 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY C 352 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 340 through 342 Processing sheet with id=AB7, first strand: chain 'C' and resid 375 through 376 removed outlier: 4.267A pdb=" N VAL C 689 " --> pdb=" O VAL C 683 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 515 through 517 removed outlier: 3.643A pdb=" N MET C 431 " --> pdb=" O VAL C 483 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 522 through 526 Processing sheet with id=AC1, first strand: chain 'C' and resid 578 through 579 removed outlier: 3.858A pdb=" N SER C 608 " --> pdb=" O ARG C 579 " (cutoff:3.500A) 856 hydrogen bonds defined for protein. 2413 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: 6.67 Time building geometry restraints manager: 5.27 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: 0.00 - 10.57: 24406 10.57 - 21.13: 5 21.13 - 31.70: 0 31.70 - 42.27: 1 42.27 - 52.84: 2 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: 359 2.69 - 3.24: 17511 3.24 - 3.79: 27490 3.79 - 4.35: 36395 4.35 - 4.90: 58396 Nonbonded interactions: 140151 Sorted by model distance: nonbonded pdb=" O VAL A 191 " pdb=" OH TYR A 310 " model vdw 2.138 3.040 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 3.040 nonbonded pdb=" OG1 THR A 122 " pdb=" O GLN A 232 " model vdw 2.208 3.040 nonbonded pdb=" OG SER 1 433 " pdb=" O PHE 1 880 " model vdw 2.221 3.040 ... (remaining 140146 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.950 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: 0.630 Check model and map are aligned: 0.100 Set scattering table: 0.160 Process input model: 53.020 Find NCS groups from input model: 0.220 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:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.420 ------------------------------------------------------------------------------- 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= 0.607 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 to be fit. rotamer outliers: 1 poor density : 230 time to evaluate : 2.121 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: 0.3143 time to fit residues: 109.0099 Evaluate side-chains 141 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 2.098 ------------------------------------------------------------------------------- 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: 9.9990 chunk 162 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 chunk 87 optimal weight: 0.8980 chunk 168 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 102 optimal weight: 30.0000 chunk 125 optimal weight: 30.0000 chunk 195 optimal weight: 0.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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 1 739 GLN 11055 ASN A 168 HIS A 275 ASN C 346 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6231 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 17952 Z= 0.295 Angle : 0.679 9.790 24414 Z= 0.349 Chirality : 0.045 0.235 2750 Planarity : 0.006 0.094 3071 Dihedral : 7.882 73.631 2579 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % 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: 0.05 (0.18), residues: 2109 helix: 0.82 (0.16), residues: 978 sheet: -0.55 (0.30), residues: 266 loop : -0.57 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP B 78 HIS 0.009 0.002 HIS B 131 PHE 0.032 0.003 PHE B 75 TYR 0.025 0.002 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 171 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 415 MET cc_start: 0.6468 (mtp) cc_final: 0.6161 (mtp) REVERT: 1 430 MET cc_start: 0.7896 (mtt) cc_final: 0.7517 (mtp) REVERT: 1 703 MET cc_start: 0.6895 (tpp) cc_final: 0.6614 (tpp) REVERT: 1 950 MET cc_start: 0.6583 (tpt) cc_final: 0.6218 (tpt) REVERT: 1 1237 LEU cc_start: 0.5019 (tp) cc_final: 0.4242 (tp) REVERT: 1 1351 SER cc_start: 0.9168 (m) cc_final: 0.8890 (t) REVERT: 1 1376 MET cc_start: 0.7579 (tpp) cc_final: 0.7203 (tpp) REVERT: 1 1404 GLN cc_start: 0.6568 (mt0) cc_final: 0.6213 (mt0) REVERT: A 158 ILE cc_start: 0.7712 (pt) cc_final: 0.7459 (mm) REVERT: A 274 TRP cc_start: 0.7649 (t-100) cc_final: 0.7253 (t-100) REVERT: A 308 THR cc_start: 0.6572 (p) cc_final: 0.6266 (t) REVERT: B 157 LYS cc_start: 0.8371 (mttt) cc_final: 0.7902 (mmmt) REVERT: B 243 LEU cc_start: 0.6827 (mp) cc_final: 0.6570 (mm) REVERT: B 430 ASP cc_start: 0.5373 (m-30) cc_final: 0.4871 (m-30) REVERT: B 470 TYR cc_start: 0.3246 (m-10) cc_final: 0.2795 (m-10) REVERT: C 281 ASN cc_start: 0.8307 (m-40) cc_final: 0.7958 (t0) REVERT: C 378 SER cc_start: 0.8244 (p) cc_final: 0.7671 (t) REVERT: C 631 MET cc_start: 0.4582 (ptm) cc_final: 0.4334 (ptm) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2822 time to fit residues: 76.7390 Evaluate side-chains 134 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 2.021 ------------------------------------------------------------------------------- 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: 10.0000 chunk 60 optimal weight: 9.9990 chunk 162 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 195 optimal weight: 0.9980 chunk 211 optimal weight: 10.0000 chunk 174 optimal weight: 0.8980 chunk 193 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 576 ASN 1 681 ASN 11055 ASN 11359 GLN A 60 ASN A 71 GLN C 346 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6195 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17952 Z= 0.199 Angle : 0.580 10.550 24414 Z= 0.294 Chirality : 0.042 0.176 2750 Planarity : 0.004 0.073 3071 Dihedral : 7.556 73.634 2579 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.05 % Allowed : 1.76 % Favored : 98.19 % 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: 0.32 (0.18), residues: 2109 helix: 1.10 (0.17), residues: 983 sheet: -0.42 (0.30), residues: 252 loop : -0.54 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 78 HIS 0.005 0.001 HIS B 131 PHE 0.021 0.002 PHE B 75 TYR 0.027 0.002 TYR C 530 ARG 0.004 0.000 ARG A 149 *********************** 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 170 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 2.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 415 MET cc_start: 0.6579 (mtp) cc_final: 0.6338 (mtp) REVERT: 1 430 MET cc_start: 0.7817 (mtt) cc_final: 0.7411 (mtp) REVERT: 1 445 TYR cc_start: 0.4388 (m-80) cc_final: 0.4157 (m-80) REVERT: 1 703 MET cc_start: 0.6876 (tpp) cc_final: 0.6661 (tpp) REVERT: 1 1237 LEU cc_start: 0.4764 (tp) cc_final: 0.3891 (tp) REVERT: 1 1351 SER cc_start: 0.9111 (m) cc_final: 0.8833 (t) REVERT: 1 1376 MET cc_start: 0.7533 (tpp) cc_final: 0.7217 (tpp) REVERT: 1 1404 GLN cc_start: 0.6674 (mt0) cc_final: 0.6263 (mt0) REVERT: A 158 ILE cc_start: 0.7726 (pt) cc_final: 0.7458 (mm) REVERT: A 274 TRP cc_start: 0.7618 (t-100) cc_final: 0.7256 (t-100) REVERT: A 308 THR cc_start: 0.6686 (p) cc_final: 0.6354 (t) REVERT: B 83 LEU cc_start: 0.6464 (tp) cc_final: 0.6106 (tt) REVERT: B 157 LYS cc_start: 0.8368 (mttt) cc_final: 0.7874 (tptt) REVERT: B 256 LEU cc_start: 0.6403 (tp) cc_final: 0.5920 (tp) REVERT: B 275 TYR cc_start: 0.6443 (t80) cc_final: 0.6203 (t80) REVERT: B 430 ASP cc_start: 0.5119 (m-30) cc_final: 0.4657 (m-30) REVERT: B 470 TYR cc_start: 0.3446 (m-10) cc_final: 0.2970 (m-10) REVERT: C 281 ASN cc_start: 0.8314 (m-40) cc_final: 0.7936 (t0) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.3061 time to fit residues: 81.1319 Evaluate side-chains 133 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.845 ------------------------------------------------------------------------------- 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: 10.0000 chunk 101 optimal weight: 30.0000 chunk 21 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 131 optimal weight: 0.9980 chunk 196 optimal weight: 0.8980 chunk 207 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11055 ASN B 332 ASN C 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6211 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17952 Z= 0.225 Angle : 0.592 9.201 24414 Z= 0.303 Chirality : 0.043 0.190 2750 Planarity : 0.004 0.065 3071 Dihedral : 7.612 73.490 2579 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.05 % Allowed : 2.50 % Favored : 97.44 % 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: 0.31 (0.18), residues: 2109 helix: 1.12 (0.17), residues: 980 sheet: -0.44 (0.31), residues: 252 loop : -0.56 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 78 HIS 0.005 0.001 HIS B 499 PHE 0.022 0.002 PHE B 75 TYR 0.020 0.002 TYR B 275 ARG 0.004 0.000 ARG A 149 *********************** 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 162 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 430 MET cc_start: 0.7677 (mtt) cc_final: 0.7257 (mtp) REVERT: 1 703 MET cc_start: 0.6847 (tpp) cc_final: 0.6512 (tpp) REVERT: 1 1237 LEU cc_start: 0.4830 (tp) cc_final: 0.3845 (tp) REVERT: 1 1351 SER cc_start: 0.9122 (m) cc_final: 0.8832 (t) REVERT: 1 1376 MET cc_start: 0.7544 (tpp) cc_final: 0.7156 (tpp) REVERT: A 158 ILE cc_start: 0.7787 (pt) cc_final: 0.7478 (mm) REVERT: A 274 TRP cc_start: 0.7653 (t-100) cc_final: 0.7374 (t-100) REVERT: A 308 THR cc_start: 0.6703 (p) cc_final: 0.6344 (t) REVERT: B 83 LEU cc_start: 0.6355 (tp) cc_final: 0.5972 (tt) REVERT: B 157 LYS cc_start: 0.8295 (mttt) cc_final: 0.7801 (tptm) REVERT: B 256 LEU cc_start: 0.6558 (tp) cc_final: 0.6339 (tp) REVERT: C 281 ASN cc_start: 0.8349 (m-40) cc_final: 0.7920 (t0) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2961 time to fit residues: 74.9928 Evaluate side-chains 126 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 2.036 ------------------------------------------------------------------------------- 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: 10.0000 chunk 117 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 154 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 177 optimal weight: 0.0010 chunk 143 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 chunk 186 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 overall best weight: 7.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11055 ASN 11359 GLN B 441 HIS ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 17952 Z= 0.418 Angle : 0.796 13.301 24414 Z= 0.410 Chirality : 0.050 0.265 2750 Planarity : 0.006 0.075 3071 Dihedral : 8.477 73.627 2579 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.05 % Allowed : 2.40 % Favored : 97.55 % 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: -0.61 (0.18), residues: 2109 helix: 0.30 (0.16), residues: 966 sheet: -0.82 (0.31), residues: 251 loop : -0.95 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 376 HIS 0.010 0.002 HIS B 293 PHE 0.033 0.003 PHE B 75 TYR 0.045 0.003 TYR B 55 ARG 0.009 0.001 ARG B 135 *********************** 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 160 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 2.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 430 MET cc_start: 0.7484 (mtt) cc_final: 0.7198 (mtp) REVERT: 1 633 ASP cc_start: 0.6339 (m-30) cc_final: 0.5873 (t0) REVERT: 1 703 MET cc_start: 0.6824 (tpp) cc_final: 0.6481 (tpp) REVERT: 1 1237 LEU cc_start: 0.4992 (tp) cc_final: 0.3894 (tp) REVERT: 1 1351 SER cc_start: 0.9126 (m) cc_final: 0.8862 (t) REVERT: 1 1376 MET cc_start: 0.7544 (tpp) cc_final: 0.7173 (tpp) REVERT: A 71 GLN cc_start: 0.6657 (mt0) cc_final: 0.6347 (mt0) REVERT: A 308 THR cc_start: 0.6602 (p) cc_final: 0.6332 (t) REVERT: B 116 PHE cc_start: 0.6760 (p90) cc_final: 0.6367 (p90) REVERT: B 157 LYS cc_start: 0.8183 (mttt) cc_final: 0.7782 (tptt) REVERT: B 243 LEU cc_start: 0.6356 (mm) cc_final: 0.6086 (mt) REVERT: B 256 LEU cc_start: 0.6645 (tp) cc_final: 0.6390 (tp) REVERT: C 281 ASN cc_start: 0.8303 (m-40) cc_final: 0.8066 (m-40) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2864 time to fit residues: 71.9727 Evaluate side-chains 125 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 2.060 ------------------------------------------------------------------------------- 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: 0.5980 chunk 187 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11316 HIS B 257 ASN C 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6200 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17952 Z= 0.185 Angle : 0.579 10.691 24414 Z= 0.295 Chirality : 0.043 0.263 2750 Planarity : 0.004 0.060 3071 Dihedral : 7.804 73.618 2579 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.05 % Allowed : 0.91 % Favored : 99.04 % 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: 0.05 (0.18), residues: 2109 helix: 0.94 (0.17), residues: 975 sheet: -0.62 (0.32), residues: 231 loop : -0.72 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 376 HIS 0.004 0.001 HIS 1 728 PHE 0.022 0.002 PHE B 75 TYR 0.017 0.001 TYR 11341 ARG 0.004 0.000 ARG 1 611 *********************** 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 168 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 703 MET cc_start: 0.6989 (tpp) cc_final: 0.6644 (tpp) REVERT: 1 1237 LEU cc_start: 0.4767 (tp) cc_final: 0.3716 (tp) REVERT: 1 1351 SER cc_start: 0.9095 (m) cc_final: 0.8804 (t) REVERT: 1 1376 MET cc_start: 0.7475 (tpp) cc_final: 0.7125 (tpp) REVERT: A 71 GLN cc_start: 0.6728 (mt0) cc_final: 0.6500 (mt0) REVERT: A 274 TRP cc_start: 0.7658 (t-100) cc_final: 0.7446 (t-100) REVERT: A 308 THR cc_start: 0.6651 (p) cc_final: 0.6434 (t) REVERT: B 83 LEU cc_start: 0.6464 (tp) cc_final: 0.6244 (tp) REVERT: B 116 PHE cc_start: 0.6730 (p90) cc_final: 0.6183 (p90) REVERT: B 157 LYS cc_start: 0.8205 (mttt) cc_final: 0.7726 (tptt) REVERT: B 181 GLN cc_start: 0.5742 (mm-40) cc_final: 0.5446 (mm-40) REVERT: B 243 LEU cc_start: 0.6002 (mm) cc_final: 0.5694 (mt) REVERT: B 256 LEU cc_start: 0.6477 (tp) cc_final: 0.6204 (tp) REVERT: B 470 TYR cc_start: 0.3175 (m-10) cc_final: 0.2884 (m-10) REVERT: C 259 ASP cc_start: 0.7049 (m-30) cc_final: 0.6770 (m-30) REVERT: C 281 ASN cc_start: 0.8296 (m-40) cc_final: 0.7839 (t0) REVERT: C 450 ASN cc_start: 0.8158 (t0) cc_final: 0.7512 (p0) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.3064 time to fit residues: 80.6038 Evaluate side-chains 135 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 2.100 ------------------------------------------------------------------------------- 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: 2.9990 chunk 23 optimal weight: 7.9990 chunk 118 optimal weight: 20.0000 chunk 151 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 116 optimal weight: 0.0980 chunk 207 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 712 GLN 11055 ASN B 257 ASN B 332 ASN ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6224 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17952 Z= 0.242 Angle : 0.612 9.883 24414 Z= 0.312 Chirality : 0.044 0.273 2750 Planarity : 0.005 0.059 3071 Dihedral : 7.893 73.501 2579 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.05 % Allowed : 1.12 % 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: -0.00 (0.18), residues: 2109 helix: 0.91 (0.17), residues: 969 sheet: -0.72 (0.33), residues: 211 loop : -0.74 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 376 HIS 0.006 0.001 HIS B 293 PHE 0.024 0.002 PHE B 75 TYR 0.021 0.002 TYR B 275 ARG 0.004 0.000 ARG A 149 *********************** 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 161 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 626 MET cc_start: 0.7289 (tmm) cc_final: 0.7042 (ttt) REVERT: 1 703 MET cc_start: 0.6788 (tpp) cc_final: 0.6432 (tpp) REVERT: 1 950 MET cc_start: 0.6766 (tpt) cc_final: 0.6494 (tpt) REVERT: 1 1237 LEU cc_start: 0.4861 (tp) cc_final: 0.3769 (tp) REVERT: 1 1351 SER cc_start: 0.9100 (m) cc_final: 0.8808 (t) REVERT: 1 1376 MET cc_start: 0.7513 (tpp) cc_final: 0.7146 (tpp) REVERT: A 71 GLN cc_start: 0.6889 (mt0) cc_final: 0.6515 (mt0) REVERT: A 114 MET cc_start: 0.6518 (mmt) cc_final: 0.6136 (mmm) REVERT: A 308 THR cc_start: 0.6654 (p) cc_final: 0.6365 (t) REVERT: B 83 LEU cc_start: 0.6393 (tp) cc_final: 0.6062 (tt) REVERT: B 116 PHE cc_start: 0.6758 (p90) cc_final: 0.6312 (p90) REVERT: B 157 LYS cc_start: 0.8248 (mttt) cc_final: 0.7799 (tptm) REVERT: B 181 GLN cc_start: 0.5793 (mm-40) cc_final: 0.5530 (mm-40) REVERT: B 243 LEU cc_start: 0.6063 (mm) cc_final: 0.5727 (mt) REVERT: B 256 LEU cc_start: 0.6536 (tp) cc_final: 0.6269 (tp) REVERT: C 252 GLN cc_start: 0.6625 (pt0) cc_final: 0.6204 (pt0) REVERT: C 259 ASP cc_start: 0.7081 (m-30) cc_final: 0.6810 (m-30) REVERT: C 281 ASN cc_start: 0.8266 (m-40) cc_final: 0.8040 (m-40) REVERT: C 450 ASN cc_start: 0.8141 (t0) cc_final: 0.7276 (m-40) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2893 time to fit residues: 73.9864 Evaluate side-chains 133 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.943 ------------------------------------------------------------------------------- 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: 5.9990 chunk 82 optimal weight: 10.0000 chunk 123 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 131 optimal weight: 0.0980 chunk 141 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 162 optimal weight: 0.0370 chunk 188 optimal weight: 10.0000 overall best weight: 3.2264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 257 ASN C 346 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6213 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17952 Z= 0.222 Angle : 0.597 12.048 24414 Z= 0.302 Chirality : 0.043 0.273 2750 Planarity : 0.004 0.058 3071 Dihedral : 7.832 73.498 2579 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.05 % Allowed : 0.64 % Favored : 99.31 % 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: 0.08 (0.18), residues: 2109 helix: 1.01 (0.17), residues: 970 sheet: -0.73 (0.34), residues: 209 loop : -0.72 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 376 HIS 0.004 0.001 HIS B 293 PHE 0.023 0.002 PHE B 75 TYR 0.017 0.002 TYR B 275 ARG 0.004 0.000 ARG A 149 *********************** 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 164 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 2.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 703 MET cc_start: 0.6947 (tpp) cc_final: 0.6659 (tmm) REVERT: 1 950 MET cc_start: 0.6962 (tpt) cc_final: 0.6724 (tpt) REVERT: 1 1351 SER cc_start: 0.9102 (m) cc_final: 0.8801 (t) REVERT: 1 1376 MET cc_start: 0.7484 (tpp) cc_final: 0.7141 (tpp) REVERT: A 114 MET cc_start: 0.6493 (mmt) cc_final: 0.6111 (mmm) REVERT: A 308 THR cc_start: 0.6657 (p) cc_final: 0.6382 (t) REVERT: B 83 LEU cc_start: 0.6313 (tp) cc_final: 0.5994 (tt) REVERT: B 116 PHE cc_start: 0.6714 (p90) cc_final: 0.6220 (p90) REVERT: B 157 LYS cc_start: 0.8217 (mttt) cc_final: 0.7757 (tptm) REVERT: B 181 GLN cc_start: 0.5781 (mm-40) cc_final: 0.5503 (mm-40) REVERT: B 243 LEU cc_start: 0.5989 (mm) cc_final: 0.5632 (mt) REVERT: B 256 LEU cc_start: 0.6535 (tp) cc_final: 0.6221 (tp) REVERT: C 252 GLN cc_start: 0.6669 (pt0) cc_final: 0.5609 (tp40) REVERT: C 259 ASP cc_start: 0.7092 (m-30) cc_final: 0.6809 (m-30) REVERT: C 281 ASN cc_start: 0.8292 (m-40) cc_final: 0.8060 (m-40) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2952 time to fit residues: 76.3370 Evaluate side-chains 130 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 2.231 ------------------------------------------------------------------------------- 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: 10.0000 chunk 181 optimal weight: 20.0000 chunk 193 optimal weight: 7.9990 chunk 116 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 151 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 chunk 174 optimal weight: 8.9990 chunk 182 optimal weight: 0.9990 chunk 192 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 347 ASN C 346 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17952 Z= 0.341 Angle : 0.722 13.093 24414 Z= 0.369 Chirality : 0.047 0.272 2750 Planarity : 0.006 0.069 3071 Dihedral : 8.360 73.555 2579 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.11 % Allowed : 0.48 % Favored : 99.41 % 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: -0.52 (0.18), residues: 2109 helix: 0.41 (0.16), residues: 974 sheet: -0.93 (0.34), residues: 210 loop : -0.93 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 325 HIS 0.008 0.002 HIS C 440 PHE 0.029 0.003 PHE B 75 TYR 0.034 0.003 TYR B 333 ARG 0.008 0.001 ARG 1 669 *********************** 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 150 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 633 ASP cc_start: 0.6332 (m-30) cc_final: 0.5769 (t0) REVERT: 1 950 MET cc_start: 0.6988 (tpt) cc_final: 0.6766 (tpt) REVERT: 1 1351 SER cc_start: 0.9095 (m) cc_final: 0.8814 (t) REVERT: 1 1376 MET cc_start: 0.7531 (tpp) cc_final: 0.7260 (tpp) REVERT: A 42 MET cc_start: 0.6479 (tmm) cc_final: 0.6271 (tmm) REVERT: A 114 MET cc_start: 0.6488 (mmt) cc_final: 0.6095 (mmm) REVERT: A 308 THR cc_start: 0.6638 (p) cc_final: 0.6376 (t) REVERT: B 157 LYS cc_start: 0.8238 (mttt) cc_final: 0.7816 (tptm) REVERT: B 236 VAL cc_start: 0.7453 (t) cc_final: 0.7201 (p) REVERT: B 256 LEU cc_start: 0.6608 (tp) cc_final: 0.6299 (tp) REVERT: C 259 ASP cc_start: 0.7060 (m-30) cc_final: 0.6836 (m-30) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.2729 time to fit residues: 64.8875 Evaluate side-chains 127 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 2.177 ------------------------------------------------------------------------------- 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: 10.0000 chunk 124 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 214 optimal weight: 10.0000 chunk 197 optimal weight: 0.2980 chunk 170 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 131 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 135 optimal weight: 0.4980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 257 ASN C 346 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6177 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17952 Z= 0.172 Angle : 0.580 13.376 24414 Z= 0.291 Chirality : 0.042 0.314 2750 Planarity : 0.004 0.058 3071 Dihedral : 7.767 73.558 2579 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.11 % Allowed : 0.21 % Favored : 99.68 % 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: 0.09 (0.18), residues: 2109 helix: 1.02 (0.17), residues: 978 sheet: -0.77 (0.34), residues: 209 loop : -0.73 (0.20), residues: 922 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 0.027 0.002 PHE B 75 TYR 0.019 0.001 TYR B 55 ARG 0.003 0.000 ARG A 149 ********************** 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 154 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 2.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 445 TYR cc_start: 0.4632 (m-80) cc_final: 0.4404 (m-80) REVERT: 1 703 MET cc_start: 0.6842 (tmm) cc_final: 0.6602 (tmm) REVERT: 1 1351 SER cc_start: 0.9029 (m) cc_final: 0.8731 (t) REVERT: 1 1376 MET cc_start: 0.7546 (tpp) cc_final: 0.7133 (tpp) REVERT: A 114 MET cc_start: 0.6583 (mmt) cc_final: 0.6227 (mmm) REVERT: A 188 LEU cc_start: 0.5844 (tp) cc_final: 0.5476 (mt) REVERT: A 308 THR cc_start: 0.6729 (p) cc_final: 0.6396 (t) REVERT: B 83 LEU cc_start: 0.6267 (tp) cc_final: 0.6044 (tp) REVERT: B 157 LYS cc_start: 0.8222 (mttt) cc_final: 0.7735 (tptm) REVERT: B 243 LEU cc_start: 0.6005 (mm) cc_final: 0.5747 (mt) REVERT: B 256 LEU cc_start: 0.6438 (tp) cc_final: 0.5853 (tp) REVERT: C 259 ASP cc_start: 0.7096 (m-30) cc_final: 0.6893 (m-30) REVERT: C 281 ASN cc_start: 0.8354 (m-40) cc_final: 0.8152 (m-40) REVERT: C 378 SER cc_start: 0.8555 (p) cc_final: 0.7756 (t) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2891 time to fit residues: 71.9189 Evaluate side-chains 124 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 2.007 ------------------------------------------------------------------------------- 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: 0.0060 chunk 52 optimal weight: 8.9990 chunk 157 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 170 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 175 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 overall best weight: 3.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3201 r_free = 0.3201 target = 0.059281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.048450 restraints weight = 329764.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.050118 restraints weight = 220701.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.051080 restraints weight = 132771.676| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17952 Z= 0.238 Angle : 0.609 11.015 24414 Z= 0.308 Chirality : 0.043 0.306 2750 Planarity : 0.005 0.057 3071 Dihedral : 7.884 73.427 2579 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.11 % Allowed : 0.32 % Favored : 99.57 % 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: 0.91 (0.17), residues: 974 sheet: -0.84 (0.34), residues: 214 loop : -0.76 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 376 HIS 0.005 0.001 HIS B 293 PHE 0.023 0.002 PHE B 75 TYR 0.019 0.002 TYR B 275 ARG 0.009 0.001 ARG 1 669 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3293.99 seconds wall clock time: 61 minutes 41.38 seconds (3701.38 seconds total)