Starting phenix.real_space_refine on Sun Jun 15 18:06:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8foj_29351/06_2025/8foj_29351.cif Found real_map, /net/cci-nas-00/data/ceres_data/8foj_29351/06_2025/8foj_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/cci-nas-00/data/ceres_data/8foj_29351/06_2025/8foj_29351.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8foj_29351/06_2025/8foj_29351.map" model { file = "/net/cci-nas-00/data/ceres_data/8foj_29351/06_2025/8foj_29351.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8foj_29351/06_2025/8foj_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 15.62, per 1000 atoms: 0.89 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: 4.07 Conformation dependent library (CDL) restraints added in 3.6 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: 7.74 Time building geometry restraints manager: 4.88 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.740 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 53.290 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.710 ------------------------------------------------------------------------------- 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 17956 Z= 0.266 Angle : 0.987 52.835 24426 Z= 0.518 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 Details of bonding type rmsd hydrogen bonds : bond 0.17054 ( 850) hydrogen bonds : angle 6.93115 ( 2413) metal coordination : bond 0.00862 ( 4) metal coordination : angle 18.18851 ( 12) covalent geometry : bond 0.00863 (17952) covalent geometry : angle 0.90080 (24414) *********************** 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 : 2.111 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: 0.3202 time to fit residues: 111.2005 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 : 2.076 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.059109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.048150 restraints weight = 310204.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.050116 restraints weight = 217091.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.051501 restraints weight = 120939.148| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 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 = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 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 17956 Z= 0.198 Angle : 0.782 31.433 24426 Z= 0.350 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 : 10.72 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 Details of bonding type rmsd hydrogen bonds : bond 0.04490 ( 850) hydrogen bonds : angle 5.60825 ( 2413) metal coordination : bond 0.00884 ( 4) metal coordination : angle 17.54857 ( 12) covalent geometry : bond 0.00451 (17952) covalent geometry : angle 0.67873 (24414) *********************** 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 : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 415 MET cc_start: 0.6004 (mtp) cc_final: 0.5505 (mtp) REVERT: 1 430 MET cc_start: 0.7864 (mtt) cc_final: 0.7119 (mtp) REVERT: 1 703 MET cc_start: 0.6363 (tpp) cc_final: 0.6155 (tpp) REVERT: 1 950 MET cc_start: 0.6267 (tpt) cc_final: 0.5928 (tpt) REVERT: 1 1121 ASN cc_start: 0.7169 (t0) cc_final: 0.6946 (t0) REVERT: 1 1237 LEU cc_start: 0.5286 (tp) cc_final: 0.4577 (tp) REVERT: 1 1351 SER cc_start: 0.9152 (m) cc_final: 0.8932 (t) REVERT: 1 1376 MET cc_start: 0.7974 (tpp) cc_final: 0.7542 (tpp) REVERT: 1 1404 GLN cc_start: 0.7222 (mt0) cc_final: 0.6967 (mt0) REVERT: A 271 LYS cc_start: 0.8836 (tptt) cc_final: 0.8506 (tppt) REVERT: A 274 TRP cc_start: 0.7697 (t-100) cc_final: 0.7033 (t-100) REVERT: A 308 THR cc_start: 0.6928 (p) cc_final: 0.6709 (t) REVERT: B 157 LYS cc_start: 0.8409 (mttt) cc_final: 0.7876 (mmmt) REVERT: B 243 LEU cc_start: 0.6991 (mp) cc_final: 0.6728 (mm) REVERT: B 430 ASP cc_start: 0.5312 (m-30) cc_final: 0.4855 (m-30) REVERT: B 470 TYR cc_start: 0.3419 (m-10) cc_final: 0.2986 (m-10) REVERT: C 259 ASP cc_start: 0.7142 (m-30) cc_final: 0.6926 (m-30) REVERT: C 281 ASN cc_start: 0.8371 (m-40) cc_final: 0.8022 (t0) REVERT: C 378 SER cc_start: 0.8370 (p) cc_final: 0.7692 (t) REVERT: C 631 MET cc_start: 0.4286 (ptm) cc_final: 0.4068 (ptm) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2818 time to fit residues: 76.7732 Evaluate side-chains 136 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 65 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 43 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 188 optimal weight: 9.9990 chunk 135 optimal weight: 0.9990 chunk 151 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 B 441 HIS C 346 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.059223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.048160 restraints weight = 327823.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.050253 restraints weight = 239223.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.051527 restraints weight = 126137.778| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17956 Z= 0.167 Angle : 0.720 30.636 24426 Z= 0.318 Chirality : 0.043 0.184 2750 Planarity : 0.005 0.078 3071 Dihedral : 7.730 73.588 2579 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % 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: 0.15 (0.18), residues: 2109 helix: 0.95 (0.16), residues: 977 sheet: -0.44 (0.31), residues: 247 loop : -0.62 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 78 HIS 0.006 0.001 HIS B 131 PHE 0.025 0.002 PHE B 75 TYR 0.030 0.002 TYR C 530 ARG 0.005 0.001 ARG A 149 Details of bonding type rmsd hydrogen bonds : bond 0.04128 ( 850) hydrogen bonds : angle 5.33775 ( 2413) metal coordination : bond 0.00792 ( 4) metal coordination : angle 16.62252 ( 12) covalent geometry : bond 0.00375 (17952) covalent geometry : angle 0.61920 (24414) *********************** 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 168 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 2.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 415 MET cc_start: 0.6302 (mtp) cc_final: 0.5813 (mtp) REVERT: 1 430 MET cc_start: 0.7907 (mtt) cc_final: 0.7195 (mtp) REVERT: 1 703 MET cc_start: 0.6428 (tpp) cc_final: 0.6203 (tpp) REVERT: 1 1237 LEU cc_start: 0.5000 (tp) cc_final: 0.4158 (tp) REVERT: 1 1351 SER cc_start: 0.9139 (m) cc_final: 0.8899 (t) REVERT: 1 1376 MET cc_start: 0.7934 (tpp) cc_final: 0.7534 (tpp) REVERT: 1 1404 GLN cc_start: 0.7261 (mt0) cc_final: 0.6956 (mt0) REVERT: A 20 LYS cc_start: 0.8379 (tttt) cc_final: 0.8125 (ttmm) REVERT: A 271 LYS cc_start: 0.8622 (tptt) cc_final: 0.8411 (tppt) REVERT: A 274 TRP cc_start: 0.7699 (t-100) cc_final: 0.7202 (t-100) REVERT: A 308 THR cc_start: 0.7036 (p) cc_final: 0.6790 (t) REVERT: B 83 LEU cc_start: 0.6968 (tp) cc_final: 0.6417 (tt) REVERT: B 116 PHE cc_start: 0.6489 (p90) cc_final: 0.6107 (p90) REVERT: B 157 LYS cc_start: 0.8331 (mttt) cc_final: 0.7796 (tptm) REVERT: B 256 LEU cc_start: 0.6669 (tp) cc_final: 0.6363 (tp) REVERT: C 281 ASN cc_start: 0.8337 (m-40) cc_final: 0.7885 (t0) REVERT: C 631 MET cc_start: 0.4249 (ptm) cc_final: 0.4008 (ptm) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.2922 time to fit residues: 76.9001 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 : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 152 optimal weight: 5.9990 chunk 32 optimal weight: 20.0000 chunk 91 optimal weight: 0.0470 chunk 176 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 108 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 chunk 112 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 overall best weight: 5.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11055 ASN B 441 HIS C 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.058105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.048249 restraints weight = 235438.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.049205 restraints weight = 163060.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.049854 restraints weight = 118453.227| |-----------------------------------------------------------------------------| r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 17956 Z= 0.246 Angle : 0.846 31.212 24426 Z= 0.384 Chirality : 0.048 0.215 2750 Planarity : 0.006 0.069 3071 Dihedral : 8.339 73.644 2579 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.05 % Allowed : 3.14 % Favored : 96.80 % 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: -0.43 (0.18), residues: 2109 helix: 0.45 (0.16), residues: 966 sheet: -0.70 (0.32), residues: 249 loop : -0.88 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 376 HIS 0.009 0.002 HIS B 293 PHE 0.030 0.003 PHE B 75 TYR 0.029 0.003 TYR 11378 ARG 0.006 0.001 ARG A 149 Details of bonding type rmsd hydrogen bonds : bond 0.04572 ( 850) hydrogen bonds : angle 5.73763 ( 2413) metal coordination : bond 0.00834 ( 4) metal coordination : angle 18.37668 ( 12) covalent geometry : bond 0.00546 (17952) covalent geometry : angle 0.74129 (24414) *********************** 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 163 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 2.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 703 MET cc_start: 0.6338 (tpp) cc_final: 0.6060 (tpp) REVERT: 1 956 TYR cc_start: 0.5668 (m-80) cc_final: 0.5337 (m-80) REVERT: 1 1237 LEU cc_start: 0.5075 (tp) cc_final: 0.4087 (tp) REVERT: 1 1351 SER cc_start: 0.9168 (m) cc_final: 0.8945 (t) REVERT: 1 1376 MET cc_start: 0.8011 (tpp) cc_final: 0.7524 (tpp) REVERT: A 20 LYS cc_start: 0.8487 (tttt) cc_final: 0.8206 (ttmm) REVERT: A 271 LYS cc_start: 0.8690 (tptt) cc_final: 0.8474 (tppt) REVERT: A 274 TRP cc_start: 0.7764 (t-100) cc_final: 0.7354 (t-100) REVERT: A 308 THR cc_start: 0.6969 (p) cc_final: 0.6748 (t) REVERT: B 116 PHE cc_start: 0.6589 (p90) cc_final: 0.6262 (p90) REVERT: B 157 LYS cc_start: 0.8256 (mttt) cc_final: 0.7726 (tptm) REVERT: B 243 LEU cc_start: 0.6606 (mt) cc_final: 0.6336 (mm) REVERT: C 259 ASP cc_start: 0.7135 (m-30) cc_final: 0.6861 (m-30) REVERT: C 281 ASN cc_start: 0.8324 (m-40) cc_final: 0.8111 (m-40) REVERT: C 613 ASP cc_start: 0.6709 (t70) cc_final: 0.6497 (t0) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2930 time to fit residues: 74.9156 Evaluate side-chains 131 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 103 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 198 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11055 ASN B 257 ASN C 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.058494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.048109 restraints weight = 305104.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.049356 restraints weight = 215990.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.050546 restraints weight = 142997.702| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 17956 Z= 0.207 Angle : 0.785 31.488 24426 Z= 0.348 Chirality : 0.046 0.255 2750 Planarity : 0.005 0.065 3071 Dihedral : 8.206 73.622 2579 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % 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: -0.45 (0.18), residues: 2109 helix: 0.51 (0.16), residues: 979 sheet: -0.78 (0.32), residues: 233 loop : -0.98 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 376 HIS 0.007 0.002 HIS 11316 PHE 0.032 0.003 PHE B 61 TYR 0.020 0.002 TYR 11341 ARG 0.005 0.001 ARG A 149 Details of bonding type rmsd hydrogen bonds : bond 0.04271 ( 850) hydrogen bonds : angle 5.59532 ( 2413) metal coordination : bond 0.01323 ( 4) metal coordination : angle 17.91505 ( 12) covalent geometry : bond 0.00459 (17952) covalent geometry : angle 0.67737 (24414) *********************** 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 167 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 703 MET cc_start: 0.6409 (tpp) cc_final: 0.6160 (tpp) REVERT: 1 956 TYR cc_start: 0.5726 (m-80) cc_final: 0.5395 (m-80) REVERT: 1 1237 LEU cc_start: 0.5012 (tp) cc_final: 0.4023 (tp) REVERT: 1 1351 SER cc_start: 0.9127 (m) cc_final: 0.8884 (t) REVERT: 1 1376 MET cc_start: 0.7958 (tpp) cc_final: 0.7516 (tpp) REVERT: A 20 LYS cc_start: 0.8524 (tttt) cc_final: 0.8253 (ttmm) REVERT: A 114 MET cc_start: 0.6867 (mmt) cc_final: 0.6574 (mmm) REVERT: A 271 LYS cc_start: 0.8661 (tptt) cc_final: 0.8346 (tppt) REVERT: B 83 LEU cc_start: 0.6980 (tp) cc_final: 0.6544 (tt) REVERT: B 110 PHE cc_start: 0.6211 (m-10) cc_final: 0.5858 (m-10) REVERT: B 116 PHE cc_start: 0.6647 (p90) cc_final: 0.6322 (p90) REVERT: B 157 LYS cc_start: 0.8249 (mttt) cc_final: 0.7721 (tptt) REVERT: B 243 LEU cc_start: 0.6515 (mt) cc_final: 0.6258 (mm) REVERT: C 450 ASN cc_start: 0.8230 (t0) cc_final: 0.7552 (p0) REVERT: C 613 ASP cc_start: 0.6721 (t70) cc_final: 0.6497 (t0) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2861 time to fit residues: 74.5522 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 : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 61 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 147 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 159 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 25 optimal weight: 8.9990 overall best weight: 5.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11055 ASN B 257 ASN B 347 ASN C 346 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.058225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.047691 restraints weight = 296874.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.049043 restraints weight = 200665.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.050187 restraints weight = 133281.648| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17956 Z= 0.224 Angle : 0.813 31.779 24426 Z= 0.361 Chirality : 0.047 0.262 2750 Planarity : 0.005 0.063 3071 Dihedral : 8.329 73.594 2579 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.05 % Allowed : 1.44 % Favored : 98.51 % 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: -0.54 (0.18), residues: 2109 helix: 0.43 (0.16), residues: 974 sheet: -1.00 (0.33), residues: 221 loop : -0.96 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP B 376 HIS 0.008 0.002 HIS B 293 PHE 0.027 0.003 PHE B 75 TYR 0.024 0.002 TYR B 275 ARG 0.005 0.001 ARG A 149 Details of bonding type rmsd hydrogen bonds : bond 0.04422 ( 850) hydrogen bonds : angle 5.70172 ( 2413) metal coordination : bond 0.01000 ( 4) metal coordination : angle 18.18879 ( 12) covalent geometry : bond 0.00499 (17952) covalent geometry : angle 0.70561 (24414) *********************** 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 150 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 2.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 703 MET cc_start: 0.6417 (tpp) cc_final: 0.6154 (tpp) REVERT: 1 747 MET cc_start: 0.8017 (tpt) cc_final: 0.7758 (tpt) REVERT: 1 950 MET cc_start: 0.6464 (tpt) cc_final: 0.6263 (tpt) REVERT: 1 956 TYR cc_start: 0.5686 (m-80) cc_final: 0.5381 (m-80) REVERT: 1 1351 SER cc_start: 0.9096 (m) cc_final: 0.8851 (t) REVERT: 1 1376 MET cc_start: 0.7962 (tpp) cc_final: 0.7561 (tpp) REVERT: A 20 LYS cc_start: 0.8444 (tttt) cc_final: 0.8196 (ttmm) REVERT: A 114 MET cc_start: 0.6706 (mmt) cc_final: 0.6305 (mmm) REVERT: A 271 LYS cc_start: 0.8623 (tptt) cc_final: 0.8173 (tppt) REVERT: B 157 LYS cc_start: 0.8242 (mttt) cc_final: 0.7675 (tptt) REVERT: B 256 LEU cc_start: 0.6694 (tp) cc_final: 0.6458 (tp) REVERT: C 259 ASP cc_start: 0.7199 (m-30) cc_final: 0.6917 (m-30) REVERT: C 281 ASN cc_start: 0.8376 (m-40) cc_final: 0.8165 (m-40) REVERT: C 613 ASP cc_start: 0.6781 (t70) cc_final: 0.6499 (t0) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.2736 time to fit residues: 66.1927 Evaluate side-chains 123 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 68 optimal weight: 3.9990 chunk 190 optimal weight: 0.0270 chunk 142 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 188 optimal weight: 9.9990 chunk 105 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 194 optimal weight: 0.8980 chunk 4 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 0.1980 overall best weight: 1.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 712 GLN B 257 ASN C 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.059784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.049317 restraints weight = 295425.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.050516 restraints weight = 190292.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.051875 restraints weight = 128488.369| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17956 Z= 0.120 Angle : 0.676 31.389 24426 Z= 0.290 Chirality : 0.042 0.275 2750 Planarity : 0.004 0.060 3071 Dihedral : 7.812 73.594 2579 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.05 % Allowed : 0.96 % Favored : 98.99 % 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: 0.04 (0.18), residues: 2109 helix: 1.02 (0.17), residues: 975 sheet: -0.85 (0.33), residues: 209 loop : -0.78 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 376 HIS 0.004 0.001 HIS B 401 PHE 0.021 0.002 PHE B 75 TYR 0.016 0.001 TYR 11341 ARG 0.003 0.000 ARG B 409 Details of bonding type rmsd hydrogen bonds : bond 0.03635 ( 850) hydrogen bonds : angle 5.14260 ( 2413) metal coordination : bond 0.00629 ( 4) metal coordination : angle 16.39599 ( 12) covalent geometry : bond 0.00267 (17952) covalent geometry : angle 0.56992 (24414) *********************** 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 to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 2.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 415 MET cc_start: 0.6135 (mtp) cc_final: 0.5704 (mtp) REVERT: 1 626 MET cc_start: 0.8177 (tmm) cc_final: 0.7935 (ttt) REVERT: 1 703 MET cc_start: 0.6552 (tpp) cc_final: 0.6275 (tpp) REVERT: 1 954 LEU cc_start: 0.7852 (pp) cc_final: 0.7581 (tt) REVERT: 1 956 TYR cc_start: 0.5820 (m-80) cc_final: 0.5475 (m-80) REVERT: 1 1351 SER cc_start: 0.9044 (m) cc_final: 0.8813 (t) REVERT: 1 1376 MET cc_start: 0.7856 (tpp) cc_final: 0.7383 (tpp) REVERT: 1 1378 TYR cc_start: 0.6763 (m-10) cc_final: 0.6531 (m-10) REVERT: A 20 LYS cc_start: 0.8434 (tttt) cc_final: 0.8072 (tppt) REVERT: A 188 LEU cc_start: 0.6206 (tp) cc_final: 0.5931 (mt) REVERT: A 271 LYS cc_start: 0.8633 (tptt) cc_final: 0.8255 (tppt) REVERT: B 83 LEU cc_start: 0.6671 (tp) cc_final: 0.6350 (tp) REVERT: B 116 PHE cc_start: 0.6778 (p90) cc_final: 0.6309 (p90) REVERT: B 157 LYS cc_start: 0.8185 (mttt) cc_final: 0.7644 (tptm) REVERT: B 162 MET cc_start: 0.7001 (tmm) cc_final: 0.6712 (tmm) REVERT: B 256 LEU cc_start: 0.6389 (tp) cc_final: 0.5957 (tp) REVERT: C 259 ASP cc_start: 0.7156 (m-30) cc_final: 0.6917 (m-30) REVERT: C 281 ASN cc_start: 0.8354 (m-40) cc_final: 0.7858 (t0) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.2826 time to fit residues: 71.7399 Evaluate side-chains 123 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 22 optimal weight: 1.9990 chunk 187 optimal weight: 7.9990 chunk 30 optimal weight: 30.0000 chunk 54 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 206 optimal weight: 9.9990 chunk 203 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 181 optimal weight: 0.0370 chunk 149 optimal weight: 10.0000 overall best weight: 2.3464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN B 257 ASN C 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.059652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.048914 restraints weight = 311622.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.050400 restraints weight = 211420.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.051680 restraints weight = 132822.104| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17956 Z= 0.132 Angle : 0.680 30.984 24426 Z= 0.293 Chirality : 0.042 0.277 2750 Planarity : 0.004 0.059 3071 Dihedral : 7.752 73.453 2579 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.11 % Allowed : 0.69 % Favored : 99.20 % 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: 0.19 (0.18), residues: 2109 helix: 1.17 (0.17), residues: 968 sheet: -0.73 (0.33), residues: 219 loop : -0.72 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 325 HIS 0.004 0.001 HIS B 293 PHE 0.021 0.002 PHE 1 352 TYR 0.017 0.002 TYR 11341 ARG 0.012 0.000 ARG B 506 Details of bonding type rmsd hydrogen bonds : bond 0.03596 ( 850) hydrogen bonds : angle 5.08720 ( 2413) metal coordination : bond 0.00738 ( 4) metal coordination : angle 15.98942 ( 12) covalent geometry : bond 0.00296 (17952) covalent geometry : angle 0.57996 (24414) *********************** 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 157 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 415 MET cc_start: 0.6254 (mtp) cc_final: 0.5848 (mtp) REVERT: 1 626 MET cc_start: 0.8372 (tmm) cc_final: 0.8042 (ttp) REVERT: 1 703 MET cc_start: 0.6552 (tpp) cc_final: 0.6280 (tpp) REVERT: 1 954 LEU cc_start: 0.7899 (pp) cc_final: 0.7592 (tt) REVERT: 1 956 TYR cc_start: 0.5851 (m-80) cc_final: 0.5549 (m-80) REVERT: 1 1351 SER cc_start: 0.9067 (m) cc_final: 0.8828 (t) REVERT: 1 1376 MET cc_start: 0.7856 (tpp) cc_final: 0.7430 (tpp) REVERT: A 20 LYS cc_start: 0.8445 (tttt) cc_final: 0.8088 (tppt) REVERT: A 71 GLN cc_start: 0.6826 (mt0) cc_final: 0.6622 (mt0) REVERT: A 271 LYS cc_start: 0.8742 (tptt) cc_final: 0.8373 (tppt) REVERT: B 83 LEU cc_start: 0.6681 (tp) cc_final: 0.6328 (tp) REVERT: B 116 PHE cc_start: 0.6783 (p90) cc_final: 0.6362 (p90) REVERT: B 157 LYS cc_start: 0.8288 (mttt) cc_final: 0.7707 (tptm) REVERT: B 256 LEU cc_start: 0.6490 (tp) cc_final: 0.5980 (tp) REVERT: B 432 HIS cc_start: 0.5910 (p-80) cc_final: 0.5690 (p-80) REVERT: C 259 ASP cc_start: 0.7190 (m-30) cc_final: 0.6980 (m-30) REVERT: C 281 ASN cc_start: 0.8382 (m-40) cc_final: 0.8177 (m-40) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.2760 time to fit residues: 69.1358 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 : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 34 optimal weight: 8.9990 chunk 177 optimal weight: 0.0870 chunk 120 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 82 optimal weight: 20.0000 chunk 160 optimal weight: 9.9990 chunk 205 optimal weight: 9.9990 overall best weight: 4.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11316 HIS A 30 ASN B 441 HIS ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.058666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.048168 restraints weight = 304857.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.049569 restraints weight = 203586.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.050506 restraints weight = 132408.622| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17956 Z= 0.203 Angle : 0.775 31.588 24426 Z= 0.348 Chirality : 0.045 0.271 2750 Planarity : 0.005 0.060 3071 Dihedral : 8.155 73.462 2579 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.11 % Allowed : 0.69 % Favored : 99.20 % 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: -0.27 (0.18), residues: 2109 helix: 0.66 (0.17), residues: 976 sheet: -0.96 (0.33), residues: 223 loop : -0.80 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 376 HIS 0.010 0.002 HIS 11316 PHE 0.026 0.003 PHE B 75 TYR 0.025 0.002 TYR B 275 ARG 0.009 0.001 ARG B 506 Details of bonding type rmsd hydrogen bonds : bond 0.04188 ( 850) hydrogen bonds : angle 5.46291 ( 2413) metal coordination : bond 0.01050 ( 4) metal coordination : angle 16.84362 ( 12) covalent geometry : bond 0.00450 (17952) covalent geometry : angle 0.67950 (24414) *********************** 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 157 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 415 MET cc_start: 0.6287 (mtp) cc_final: 0.5938 (mtp) REVERT: 1 619 MET cc_start: 0.7476 (ttp) cc_final: 0.6978 (ttt) REVERT: 1 626 MET cc_start: 0.8395 (tmm) cc_final: 0.8090 (ttp) REVERT: 1 633 ASP cc_start: 0.6609 (m-30) cc_final: 0.5854 (t0) REVERT: 1 703 MET cc_start: 0.6482 (tpp) cc_final: 0.6250 (tmm) REVERT: 1 956 TYR cc_start: 0.5882 (m-80) cc_final: 0.5587 (m-80) REVERT: 1 1351 SER cc_start: 0.9098 (m) cc_final: 0.8864 (t) REVERT: 1 1376 MET cc_start: 0.7948 (tpp) cc_final: 0.7565 (tpp) REVERT: A 20 LYS cc_start: 0.8380 (tttt) cc_final: 0.8085 (tppt) REVERT: A 71 GLN cc_start: 0.6923 (mt0) cc_final: 0.6722 (mt0) REVERT: A 271 LYS cc_start: 0.8668 (tptt) cc_final: 0.8244 (tppt) REVERT: B 157 LYS cc_start: 0.8281 (mttt) cc_final: 0.7717 (tptm) REVERT: B 256 LEU cc_start: 0.6667 (tp) cc_final: 0.6348 (tp) REVERT: B 376 TRP cc_start: 0.5228 (m-90) cc_final: 0.5009 (m-90) REVERT: C 252 GLN cc_start: 0.6823 (pt0) cc_final: 0.6303 (pt0) REVERT: C 259 ASP cc_start: 0.7144 (m-30) cc_final: 0.6881 (m-30) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.3008 time to fit residues: 76.3778 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 : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 161 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 79 optimal weight: 0.0870 chunk 205 optimal weight: 1.9990 chunk 44 optimal weight: 0.1980 chunk 179 optimal weight: 20.0000 chunk 30 optimal weight: 8.9990 chunk 126 optimal weight: 4.9990 chunk 93 optimal weight: 0.1980 chunk 136 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11316 HIS A 30 ASN B 257 ASN C 346 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.060003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.049371 restraints weight = 312113.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.050673 restraints weight = 213508.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.051836 restraints weight = 139923.958| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17956 Z= 0.121 Angle : 0.677 30.595 24426 Z= 0.294 Chirality : 0.043 0.310 2750 Planarity : 0.004 0.059 3071 Dihedral : 7.764 73.510 2579 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % 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: 0.14 (0.18), residues: 2109 helix: 1.11 (0.17), residues: 971 sheet: -0.75 (0.33), residues: 219 loop : -0.73 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 376 HIS 0.004 0.001 HIS B 401 PHE 0.027 0.002 PHE B 132 TYR 0.031 0.002 TYR B 55 ARG 0.012 0.000 ARG B 506 Details of bonding type rmsd hydrogen bonds : bond 0.03550 ( 850) hydrogen bonds : angle 5.06362 ( 2413) metal coordination : bond 0.00571 ( 4) metal coordination : angle 15.51138 ( 12) covalent geometry : bond 0.00269 (17952) covalent geometry : angle 0.58323 (24414) ********************** 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 162 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 415 MET cc_start: 0.6167 (mtp) cc_final: 0.5791 (mtp) REVERT: 1 619 MET cc_start: 0.7463 (ttp) cc_final: 0.7244 (ttp) REVERT: 1 626 MET cc_start: 0.8419 (tmm) cc_final: 0.8103 (ttp) REVERT: 1 703 MET cc_start: 0.6686 (tpp) cc_final: 0.6371 (tmm) REVERT: 1 954 LEU cc_start: 0.7889 (pp) cc_final: 0.7671 (tt) REVERT: 1 956 TYR cc_start: 0.5959 (m-80) cc_final: 0.5640 (m-80) REVERT: 1 1351 SER cc_start: 0.9052 (m) cc_final: 0.8804 (t) REVERT: 1 1376 MET cc_start: 0.7848 (tpp) cc_final: 0.7361 (tpp) REVERT: A 20 LYS cc_start: 0.8479 (tttt) cc_final: 0.8109 (tppt) REVERT: A 188 LEU cc_start: 0.5942 (tp) cc_final: 0.5563 (mt) REVERT: A 271 LYS cc_start: 0.8687 (tptt) cc_final: 0.8317 (tppt) REVERT: B 83 LEU cc_start: 0.6647 (tp) cc_final: 0.6387 (tp) REVERT: B 116 PHE cc_start: 0.6775 (p90) cc_final: 0.6293 (p90) REVERT: B 157 LYS cc_start: 0.8201 (mttt) cc_final: 0.7647 (tptm) REVERT: B 256 LEU cc_start: 0.6478 (tp) cc_final: 0.5872 (tp) REVERT: C 259 ASP cc_start: 0.7210 (m-30) cc_final: 0.7003 (m-30) REVERT: C 378 SER cc_start: 0.8632 (p) cc_final: 0.7768 (t) REVERT: C 626 PHE cc_start: 0.7073 (m-10) cc_final: 0.6841 (m-10) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2806 time to fit residues: 72.0549 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 : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 158 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 106 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 198 optimal weight: 8.9990 chunk 73 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 189 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 56 optimal weight: 0.0010 overall best weight: 2.5792 ------------------------------------------------------------------------------- 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 = 0.3216 r_free = 0.3216 target = 0.059770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.049813 restraints weight = 247850.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.051566 restraints weight = 158601.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.052242 restraints weight = 96628.152| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17956 Z= 0.134 Angle : 0.674 30.170 24426 Z= 0.294 Chirality : 0.043 0.308 2750 Planarity : 0.004 0.058 3071 Dihedral : 7.747 73.422 2579 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % 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: 0.19 (0.18), residues: 2109 helix: 1.13 (0.17), residues: 973 sheet: -0.70 (0.34), residues: 219 loop : -0.71 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 376 HIS 0.004 0.001 HIS B 293 PHE 0.022 0.002 PHE B 75 TYR 0.018 0.002 TYR B 55 ARG 0.011 0.000 ARG 1 669 Details of bonding type rmsd hydrogen bonds : bond 0.03581 ( 850) hydrogen bonds : angle 5.03436 ( 2413) metal coordination : bond 0.00680 ( 4) metal coordination : angle 15.36347 ( 12) covalent geometry : bond 0.00302 (17952) covalent geometry : angle 0.58234 (24414) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5514.84 seconds wall clock time: 97 minutes 5.73 seconds (5825.73 seconds total)