Starting phenix.real_space_refine on Thu Aug 6 20:09:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vnv_43361/08_2026/8vnv_43361.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vnv_43361/08_2026/8vnv_43361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vnv_43361/08_2026/8vnv_43361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vnv_43361/08_2026/8vnv_43361.map" model { file = "/net/cci-nas-00/data/ceres_data/8vnv_43361/08_2026/8vnv_43361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vnv_43361/08_2026/8vnv_43361.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1328 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 49 5.49 5 S 95 5.16 5 C 9928 2.51 5 N 2871 2.21 5 O 2984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15927 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3340 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 19, 'TRANS': 419} Chain breaks: 7 Unresolved non-hydrogen bonds: 294 Unresolved non-hydrogen angles: 356 Unresolved non-hydrogen dihedrals: 234 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 9, 'GLU:plan': 16, 'GLN:plan1': 9, 'ASN:plan1': 9, 'HIS:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 184 Chain: "L" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2874 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 349} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "N" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3080 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 22, 'TRANS': 372} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 4278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4278 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 33, 'TRANS': 572} Chain breaks: 2 Unresolved non-hydrogen bonds: 604 Unresolved non-hydrogen angles: 753 Unresolved non-hydrogen dihedrals: 486 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'ARG:plan': 16, 'GLU:plan': 27, 'TYR:plan': 5, 'GLN:plan1': 10, 'PHE:plan': 6, 'ASP:plan': 15, 'ASN:plan1': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 372 Chain: "B" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 290 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 36} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'M3L:plan-1': 1, 'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "P" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 873 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 7, 'TRANS': 109} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 5, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 55 Chain: "H" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 470 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "I" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 159 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 19} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 537 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 3.50, per 1000 atoms: 0.22 Number of scatterers: 15927 At special positions: 0 Unit cell: (160.65, 130.2, 113.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 95 16.00 P 49 15.00 O 2984 8.00 N 2871 7.00 C 9928 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 286 " - pdb=" SG CYS C 294 " distance=2.02 Simple disulfide: pdb=" SG CYS C 523 " - pdb=" SG CYS C 536 " distance=2.03 Simple disulfide: pdb=" SG CYS C 530 " - pdb=" SG CYS C 549 " distance=2.03 Simple disulfide: pdb=" SG CYS C 530 " - pdb=" SG CYS C 553 " distance=2.03 Simple disulfide: pdb=" SG CYS C 549 " - pdb=" SG CYS C 553 " distance=2.03 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: 1.46 Conformation dependent library (CDL) restraints added in 712.7 milliseconds 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3792 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 23 sheets defined 25.6% alpha, 20.7% beta 20 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 83 through 107 Proline residue: A 93 - end of helix removed outlier: 4.095A pdb=" N ILE A 96 " --> pdb=" O LYS A 92 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR A 102 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 119 removed outlier: 6.182A pdb=" N THR A 116 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N TYR A 117 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER A 119 " --> pdb=" O THR A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 146 Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 459 through 470 Processing helix chain 'A' and resid 503 through 508 removed outlier: 4.375A pdb=" N HIS A 507 " --> pdb=" O PRO A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 543 Processing helix chain 'A' and resid 576 through 580 Processing helix chain 'A' and resid 589 through 602 removed outlier: 4.011A pdb=" N ILE A 600 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU A 601 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU A 602 " --> pdb=" O THR A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 623 removed outlier: 3.875A pdb=" N VAL A 613 " --> pdb=" O GLY A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 651 removed outlier: 4.675A pdb=" N HIS A 634 " --> pdb=" O ASN A 630 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLN A 645 " --> pdb=" O GLU A 641 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LYS A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 665 Processing helix chain 'A' and resid 670 through 682 removed outlier: 3.810A pdb=" N ILE A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASP A 675 " --> pdb=" O ILE A 671 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS A 676 " --> pdb=" O MET A 672 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG A 682 " --> pdb=" O VAL A 678 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 130 No H-bonds generated for 'chain 'L' and resid 128 through 130' Processing helix chain 'L' and resid 267 through 279 removed outlier: 3.656A pdb=" N TYR L 278 " --> pdb=" O ILE L 274 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP L 279 " --> pdb=" O LYS L 275 " (cutoff:3.500A) Processing helix chain 'L' and resid 395 through 399 removed outlier: 3.835A pdb=" N ALA L 399 " --> pdb=" O PRO L 396 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 28 Processing helix chain 'N' and resid 155 through 157 No H-bonds generated for 'chain 'N' and resid 155 through 157' Processing helix chain 'N' and resid 210 through 214 removed outlier: 4.262A pdb=" N GLY N 214 " --> pdb=" O PRO N 211 " (cutoff:3.500A) Processing helix chain 'N' and resid 348 through 350 No H-bonds generated for 'chain 'N' and resid 348 through 350' Processing helix chain 'N' and resid 355 through 362 Processing helix chain 'N' and resid 406 through 409 Processing helix chain 'C' and resid 18 through 62 removed outlier: 4.416A pdb=" N LEU C 29 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 142 removed outlier: 3.563A pdb=" N ASP C 142 " --> pdb=" O LEU C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 153 removed outlier: 4.044A pdb=" N GLU C 147 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 178 Processing helix chain 'C' and resid 221 through 231 Processing helix chain 'C' and resid 236 through 250 removed outlier: 3.906A pdb=" N LEU C 240 " --> pdb=" O THR C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 278 Processing helix chain 'C' and resid 278 through 284 Processing helix chain 'C' and resid 328 through 338 removed outlier: 3.624A pdb=" N ALA C 336 " --> pdb=" O LYS C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 448 removed outlier: 3.882A pdb=" N GLY C 445 " --> pdb=" O ARG C 441 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N THR C 446 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR C 447 " --> pdb=" O LEU C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 457 Processing helix chain 'C' and resid 462 through 474 Processing helix chain 'C' and resid 475 through 477 No H-bonds generated for 'chain 'C' and resid 475 through 477' Processing helix chain 'C' and resid 494 through 510 removed outlier: 3.613A pdb=" N LEU C 498 " --> pdb=" O ARG C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 514 Processing helix chain 'C' and resid 534 through 539 Processing helix chain 'C' and resid 571 through 576 removed outlier: 3.549A pdb=" N ALA C 576 " --> pdb=" O PRO C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 609 Processing helix chain 'C' and resid 648 through 662 removed outlier: 3.883A pdb=" N VAL C 657 " --> pdb=" O ARG C 653 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS C 660 " --> pdb=" O LYS C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 687 removed outlier: 3.511A pdb=" N ARG C 685 " --> pdb=" O ASN C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 737 Processing helix chain 'B' and resid 144 through 151 removed outlier: 3.952A pdb=" N SER B 148 " --> pdb=" O ILE B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 166 Processing helix chain 'P' and resid 191 through 210 removed outlier: 3.630A pdb=" N ALA P 197 " --> pdb=" O GLN P 193 " (cutoff:3.500A) Processing helix chain 'P' and resid 257 through 259 No H-bonds generated for 'chain 'P' and resid 257 through 259' Processing helix chain 'P' and resid 270 through 272 No H-bonds generated for 'chain 'P' and resid 270 through 272' Processing helix chain 'P' and resid 277 through 281 Processing sheet with id=AA1, first strand: chain 'A' and resid 230 through 232 removed outlier: 3.837A pdb=" N GLU A 314 " --> pdb=" O LYS P 231 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS P 231 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ILE P 227 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA P 228 " --> pdb=" O LEU P 240 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 203 through 211 removed outlier: 3.568A pdb=" N THR A 208 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N VAL A 186 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N LYS A 210 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU A 184 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLU A 185 " --> pdb=" O PHE A 252 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N PHE A 252 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU A 187 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LEU A 250 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL A 189 " --> pdb=" O TYR A 248 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N TYR A 248 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL A 191 " --> pdb=" O LYS A 246 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 438 through 444 removed outlier: 4.595A pdb=" N ILE A 428 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ARG A 427 " --> pdb=" O ALA A 485 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ILE A 487 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N PHE A 429 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL A 489 " --> pdb=" O PHE A 429 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N GLN A 431 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ILE A 491 " --> pdb=" O GLN A 431 " (cutoff:3.500A) removed outlier: 9.354A pdb=" N LEU A 433 " --> pdb=" O ILE A 491 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 557 through 560 removed outlier: 3.689A pdb=" N ILE A 525 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL N 35 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE N 398 " --> pdb=" O SER N 394 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N VAL N 389 " --> pdb=" O TRP N 382 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N TRP N 382 " --> pdb=" O VAL N 389 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N CYS N 391 " --> pdb=" O PHE N 380 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N PHE N 380 " --> pdb=" O CYS N 391 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL N 393 " --> pdb=" O SER N 378 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 413 through 418 removed outlier: 4.277A pdb=" N GLN L 415 " --> pdb=" O VAL L 428 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER L 433 " --> pdb=" O CYS L 429 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASN L 86 " --> pdb=" O ARG L 436 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ASP L 438 " --> pdb=" O CYS L 84 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N CYS L 84 " --> pdb=" O ASP L 438 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 96 through 101 removed outlier: 5.784A pdb=" N GLY L 98 " --> pdb=" O VAL L 116 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N VAL L 116 " --> pdb=" O GLY L 98 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU L 111 " --> pdb=" O CYS L 126 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU L 123 " --> pdb=" O GLN L 136 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLN L 136 " --> pdb=" O LEU L 123 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLU L 125 " --> pdb=" O LEU L 134 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LEU L 134 " --> pdb=" O GLU L 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 151 through 154 removed outlier: 3.951A pdb=" N LYS L 184 " --> pdb=" O ILE L 174 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASN L 176 " --> pdb=" O CYS L 182 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N CYS L 182 " --> pdb=" O ASN L 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 193 through 198 removed outlier: 6.351A pdb=" N VAL L 209 " --> pdb=" O ASN L 194 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU L 196 " --> pdb=" O LEU L 207 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU L 207 " --> pdb=" O LEU L 196 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE L 198 " --> pdb=" O LEU L 205 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LEU L 205 " --> pdb=" O PHE L 198 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER L 210 " --> pdb=" O ALA L 214 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA L 214 " --> pdb=" O SER L 210 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ILE L 228 " --> pdb=" O ILE L 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 239 through 244 removed outlier: 3.582A pdb=" N SER L 241 " --> pdb=" O CYS L 254 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET L 252 " --> pdb=" O ASP L 243 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE L 299 " --> pdb=" O LEU L 262 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 309 through 315 removed outlier: 3.691A pdb=" N CYS L 311 " --> pdb=" O LYS L 322 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER L 323 " --> pdb=" O ALA L 327 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA L 327 " --> pdb=" O SER L 323 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE L 328 " --> pdb=" O ARG L 355 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ARG L 355 " --> pdb=" O ILE L 328 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N CYS L 330 " --> pdb=" O LEU L 353 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 368 through 370 Processing sheet with id=AB3, first strand: chain 'N' and resid 48 through 54 removed outlier: 5.206A pdb=" N ARG N 65 " --> pdb=" O LEU N 50 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ASP N 52 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE N 63 " --> pdb=" O ASP N 52 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N THR N 54 " --> pdb=" O PHE N 61 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N PHE N 61 " --> pdb=" O THR N 54 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N SER N 83 " --> pdb=" O ILE N 117 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ILE N 117 " --> pdb=" O SER N 83 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N GLN N 85 " --> pdb=" O ILE N 115 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE N 115 " --> pdb=" O GLN N 85 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 129 through 132 removed outlier: 3.654A pdb=" N ARG N 129 " --> pdb=" O LYS N 143 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ARG N 172 " --> pdb=" O VAL N 217 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 182 through 185 removed outlier: 4.001A pdb=" N SER N 184 " --> pdb=" O LEU N 194 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU N 194 " --> pdb=" O SER N 184 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 230 through 235 removed outlier: 3.810A pdb=" N ASP N 232 " --> pdb=" O VAL N 246 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL N 246 " --> pdb=" O ASP N 232 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS N 251 " --> pdb=" O ALA N 247 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 276 through 281 removed outlier: 3.817A pdb=" N CYS N 278 " --> pdb=" O GLY N 292 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N HIS N 311 " --> pdb=" O LEU N 300 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ASP N 302 " --> pdb=" O LYS N 309 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N LYS N 309 " --> pdb=" O ASP N 302 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 320 through 325 removed outlier: 6.147A pdb=" N ASP N 346 " --> pdb=" O LEU N 366 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LEU N 366 " --> pdb=" O ASP N 346 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 114 through 115 removed outlier: 5.930A pdb=" N SER C 114 " --> pdb=" O GLY C 681 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 120 through 121 removed outlier: 6.111A pdb=" N PHE C 120 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N SER C 647 " --> pdb=" O PHE C 120 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 285 through 286 removed outlier: 3.598A pdb=" N LYS C 291 " --> pdb=" O CYS C 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 614 through 618 removed outlier: 4.006A pdb=" N GLU C 720 " --> pdb=" O ILE C 628 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 637 through 640 removed outlier: 7.001A pdb=" N PHE C 637 " --> pdb=" O ALA C 712 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ALA C 712 " --> pdb=" O PHE C 637 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER C 639 " --> pdb=" O ILE C 710 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 219 through 223 removed outlier: 3.521A pdb=" N VAL P 267 " --> pdb=" O VAL P 220 " (cutoff:3.500A) 511 hydrogen bonds defined for protein. 1404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 3.52 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5091 1.34 - 1.46: 3486 1.46 - 1.58: 7609 1.58 - 1.70: 96 1.70 - 1.82: 131 Bond restraints: 16413 Sorted by residual: bond pdb=" C3' DC D 162 " pdb=" C2' DC D 162 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 bond pdb=" C3' DG H 152 " pdb=" C2' DG H 152 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.77e+00 bond pdb=" C3' DG D 161 " pdb=" O3' DG D 161 " ideal model delta sigma weight residual 1.435 1.474 -0.039 1.30e-02 5.92e+03 8.97e+00 bond pdb=" C2 SAH C 801 " pdb=" N3 SAH C 801 " ideal model delta sigma weight residual 1.322 1.381 -0.059 2.00e-02 2.50e+03 8.63e+00 bond pdb=" C3' DG D 165 " pdb=" C2' DG D 165 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.87e+00 ... (remaining 16408 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 22002 2.07 - 4.15: 461 4.15 - 6.22: 55 6.22 - 8.30: 11 8.30 - 10.37: 8 Bond angle restraints: 22537 Sorted by residual: angle pdb=" N3 DT D 170 " pdb=" C4 DT D 170 " pdb=" O4 DT D 170 " ideal model delta sigma weight residual 119.90 122.66 -2.76 6.00e-01 2.78e+00 2.12e+01 angle pdb=" C LEU L 225 " pdb=" N VAL L 226 " pdb=" CA VAL L 226 " ideal model delta sigma weight residual 122.96 118.85 4.11 9.50e-01 1.11e+00 1.87e+01 angle pdb=" N3 DT H 140 " pdb=" C4 DT H 140 " pdb=" O4 DT H 140 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT H 142 " pdb=" C4 DT H 142 " pdb=" O4 DT H 142 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" O4 DT D 170 " pdb=" C4 DT D 170 " pdb=" C5 DT D 170 " ideal model delta sigma weight residual 124.90 121.95 2.95 7.00e-01 2.04e+00 1.78e+01 ... (remaining 22532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.16: 9187 35.16 - 70.33: 409 70.33 - 105.49: 18 105.49 - 140.65: 1 140.65 - 175.82: 7 Dihedral angle restraints: 9622 sinusoidal: 3813 harmonic: 5809 Sorted by residual: dihedral pdb=" CB CYS C 549 " pdb=" SG CYS C 549 " pdb=" SG CYS C 553 " pdb=" CB CYS C 553 " ideal model delta sinusoidal sigma weight residual -86.00 3.13 -89.13 1 1.00e+01 1.00e-02 9.45e+01 dihedral pdb=" CB CYS C 530 " pdb=" SG CYS C 530 " pdb=" SG CYS C 549 " pdb=" CB CYS C 549 " ideal model delta sinusoidal sigma weight residual 93.00 173.73 -80.73 1 1.00e+01 1.00e-02 8.05e+01 dihedral pdb=" CB CYS C 530 " pdb=" SG CYS C 530 " pdb=" SG CYS C 553 " pdb=" CB CYS C 553 " ideal model delta sinusoidal sigma weight residual -86.00 -157.11 71.11 1 1.00e+01 1.00e-02 6.49e+01 ... (remaining 9619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2022 0.053 - 0.105: 404 0.105 - 0.158: 89 0.158 - 0.210: 3 0.210 - 0.263: 1 Chirality restraints: 2519 Sorted by residual: chirality pdb=" CB THR L 149 " pdb=" CA THR L 149 " pdb=" OG1 THR L 149 " pdb=" CG2 THR L 149 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C3' DG D 167 " pdb=" C4' DG D 167 " pdb=" O3' DG D 167 " pdb=" C2' DG D 167 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.17 2.00e-01 2.50e+01 6.85e-01 chirality pdb=" C3' DG H 135 " pdb=" C4' DG H 135 " pdb=" O3' DG H 135 " pdb=" C2' DG H 135 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.75e-01 ... (remaining 2516 not shown) Planarity restraints: 2743 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 572 " -0.041 5.00e-02 4.00e+02 6.22e-02 6.20e+00 pdb=" N PRO A 573 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 573 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 573 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR L 148 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.59e+00 pdb=" C TYR L 148 " 0.041 2.00e-02 2.50e+03 pdb=" O TYR L 148 " -0.015 2.00e-02 2.50e+03 pdb=" N THR L 149 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 499 " -0.015 2.00e-02 2.50e+03 1.36e-02 4.64e+00 pdb=" CG TRP C 499 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP C 499 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP C 499 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 499 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 499 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 499 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 499 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 499 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 499 " 0.000 2.00e-02 2.50e+03 ... (remaining 2740 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 333 2.67 - 3.22: 15264 3.22 - 3.78: 26344 3.78 - 4.34: 34337 4.34 - 4.90: 54406 Nonbonded interactions: 130684 Sorted by model distance: nonbonded pdb=" N2 DG H 149 " pdb=" O2 DC D 166 " model vdw 2.107 2.496 nonbonded pdb=" OE1 GLN L 136 " pdb=" OH TYR L 138 " model vdw 2.120 3.040 nonbonded pdb=" OH TYR L 308 " pdb=" O ILE C 131 " model vdw 2.142 3.040 nonbonded pdb=" NE2 GLN C 717 " pdb=" OE2 GLU C 720 " model vdw 2.195 3.120 nonbonded pdb=" OG SER N 44 " pdb=" O GLY N 69 " model vdw 2.200 3.040 ... (remaining 130679 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.840 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 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 : 0.003 0.066 16418 Z= 0.227 Angle : 0.709 10.369 22547 Z= 0.420 Chirality : 0.044 0.263 2519 Planarity : 0.004 0.071 2743 Dihedral : 18.710 175.816 5815 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.48 % Allowed : 20.84 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.19), residues: 1941 helix: 0.97 (0.27), residues: 396 sheet: 0.08 (0.25), residues: 412 loop : -0.69 (0.19), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 52 TYR 0.010 0.001 TYR N 21 PHE 0.024 0.001 PHE P 190 TRP 0.037 0.002 TRP C 499 HIS 0.005 0.001 HIS C 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.23 (16413) covalent geometry : angle 0.70764 / 0.42 (22537) SS BOND : bond 0.00345 / 0.18 ( 5) SS BOND : angle 2.46990 / 1.55 ( 10) hydrogen bonds : bond 0.21581 / 14.73 ( 564) hydrogen bonds : angle 7.73986 / 5.36 ( 1506) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 162 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 632 MET cc_start: 0.7258 (mmt) cc_final: 0.6872 (mmt) outliers start: 7 outliers final: 2 residues processed: 163 average time/residue: 0.1229 time to fit residues: 31.1870 Evaluate side-chains 156 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain P residue 221 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 30.0000 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 194 ASN N 18 ASN N 85 GLN N 328 HIS C 717 GLN ** P 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.110216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.091467 restraints weight = 63008.730| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 4.58 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.0735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16418 Z= 0.132 Angle : 0.638 7.429 22547 Z= 0.335 Chirality : 0.047 0.309 2519 Planarity : 0.004 0.052 2743 Dihedral : 18.428 175.915 2627 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.95 % Allowed : 19.26 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.19), residues: 1941 helix: 0.79 (0.26), residues: 413 sheet: -0.09 (0.24), residues: 441 loop : -0.66 (0.20), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 355 TYR 0.010 0.001 TYR C 448 PHE 0.018 0.001 PHE C 290 TRP 0.020 0.001 TRP L 314 HIS 0.005 0.001 HIS N 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (16413) covalent geometry : angle 0.63713 / 0.33 (22537) SS BOND : bond 0.00228 / 0.12 ( 5) SS BOND : angle 2.01688 / 1.25 ( 10) hydrogen bonds : bond 0.05557 / 3.96 ( 564) hydrogen bonds : angle 6.13956 / 4.21 ( 1506) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 153 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8198 (mt) cc_final: 0.7891 (mt) REVERT: A 184 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7240 (tt) REVERT: A 637 MET cc_start: 0.8499 (mtp) cc_final: 0.8256 (mtt) REVERT: L 189 HIS cc_start: 0.7711 (OUTLIER) cc_final: 0.6830 (t-90) REVERT: N 133 MET cc_start: 0.6087 (tpp) cc_final: 0.5848 (tpp) REVERT: C 110 MET cc_start: 0.9190 (tmm) cc_final: 0.8658 (tmm) REVERT: C 439 MET cc_start: 0.6846 (tmm) cc_final: 0.6401 (tmm) outliers start: 43 outliers final: 24 residues processed: 185 average time/residue: 0.1205 time to fit residues: 35.1435 Evaluate side-chains 171 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain L residue 92 HIS Chi-restraints excluded: chain L residue 126 CYS Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 182 CYS Chi-restraints excluded: chain L residue 189 HIS Chi-restraints excluded: chain L residue 320 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 85 GLN Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain N residue 399 MET Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain P residue 190 PHE Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain P residue 239 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 chunk 131 optimal weight: 0.0770 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 ASN N 85 GLN P 193 GLN ** P 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.108418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.089551 restraints weight = 63955.826| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 4.56 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16418 Z= 0.155 Angle : 0.629 9.312 22547 Z= 0.328 Chirality : 0.047 0.315 2519 Planarity : 0.004 0.049 2743 Dihedral : 18.414 175.359 2624 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.08 % Allowed : 19.47 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.20), residues: 1941 helix: 0.81 (0.26), residues: 413 sheet: -0.29 (0.24), residues: 437 loop : -0.69 (0.20), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 355 TYR 0.015 0.001 TYR L 154 PHE 0.018 0.001 PHE L 97 TRP 0.033 0.002 TRP C 499 HIS 0.005 0.001 HIS N 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (16413) covalent geometry : angle 0.62752 / 0.33 (22537) SS BOND : bond 0.00424 / 0.22 ( 5) SS BOND : angle 2.05548 / 1.27 ( 10) hydrogen bonds : bond 0.05044 / 3.59 ( 564) hydrogen bonds : angle 5.74816 / 3.96 ( 1506) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 151 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8242 (mt) cc_final: 0.7916 (mt) REVERT: A 637 MET cc_start: 0.8517 (mtp) cc_final: 0.8274 (mtt) REVERT: L 131 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8098 (tm-30) REVERT: L 148 TYR cc_start: 0.7463 (OUTLIER) cc_final: 0.7062 (p90) REVERT: L 189 HIS cc_start: 0.7781 (OUTLIER) cc_final: 0.6863 (t-90) REVERT: N 133 MET cc_start: 0.6173 (tpp) cc_final: 0.5933 (tpp) REVERT: C 52 ARG cc_start: 0.7010 (mmp80) cc_final: 0.6672 (mmp80) REVERT: C 134 MET cc_start: 0.8343 (ppp) cc_final: 0.8061 (ppp) REVERT: C 439 MET cc_start: 0.6936 (tmm) cc_final: 0.6720 (tmm) REVERT: C 593 HIS cc_start: 0.8234 (m-70) cc_final: 0.8030 (t-90) REVERT: C 701 MET cc_start: 0.7667 (tpp) cc_final: 0.7389 (mpp) outliers start: 45 outliers final: 29 residues processed: 187 average time/residue: 0.1178 time to fit residues: 34.7850 Evaluate side-chains 174 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain L residue 92 HIS Chi-restraints excluded: chain L residue 126 CYS Chi-restraints excluded: chain L residue 131 GLU Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 182 CYS Chi-restraints excluded: chain L residue 189 HIS Chi-restraints excluded: chain L residue 300 SER Chi-restraints excluded: chain L residue 320 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 183 LEU Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain N residue 394 SER Chi-restraints excluded: chain N residue 399 MET Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 653 ARG Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain P residue 190 PHE Chi-restraints excluded: chain P residue 220 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 198 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 162 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 188 optimal weight: 0.6980 chunk 137 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 HIS N 18 ASN ** N 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.108008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.089012 restraints weight = 63149.841| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 4.53 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16418 Z= 0.137 Angle : 0.606 10.972 22547 Z= 0.316 Chirality : 0.047 0.328 2519 Planarity : 0.004 0.048 2743 Dihedral : 18.370 175.549 2624 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.98 % Allowed : 19.67 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.20), residues: 1941 helix: 0.82 (0.26), residues: 415 sheet: -0.44 (0.24), residues: 441 loop : -0.68 (0.20), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 355 TYR 0.011 0.001 TYR C 448 PHE 0.015 0.001 PHE L 97 TRP 0.014 0.001 TRP L 314 HIS 0.006 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (16413) covalent geometry : angle 0.60462 / 0.32 (22537) SS BOND : bond 0.00215 / 0.11 ( 5) SS BOND : angle 2.03452 / 1.24 ( 10) hydrogen bonds : bond 0.04672 / 3.35 ( 564) hydrogen bonds : angle 5.46737 / 3.76 ( 1506) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 156 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8221 (mt) cc_final: 0.7900 (mt) REVERT: A 637 MET cc_start: 0.8544 (mtp) cc_final: 0.8304 (mtt) REVERT: L 131 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8047 (tm-30) REVERT: L 148 TYR cc_start: 0.7474 (OUTLIER) cc_final: 0.7005 (p90) REVERT: L 189 HIS cc_start: 0.7783 (OUTLIER) cc_final: 0.6890 (t-90) REVERT: L 366 MET cc_start: 0.6541 (mtm) cc_final: 0.6191 (mtm) REVERT: N 59 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.9052 (ptpp) REVERT: N 133 MET cc_start: 0.6109 (tpp) cc_final: 0.5831 (tpp) REVERT: N 253 MET cc_start: 0.4955 (ptm) cc_final: 0.4341 (ppp) REVERT: C 134 MET cc_start: 0.8243 (ppp) cc_final: 0.7943 (ppp) REVERT: C 574 TYR cc_start: 0.8698 (t80) cc_final: 0.8320 (t80) REVERT: C 593 HIS cc_start: 0.8256 (m-70) cc_final: 0.8053 (t-90) REVERT: C 653 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7126 (mtm-85) REVERT: C 701 MET cc_start: 0.7656 (tpp) cc_final: 0.7361 (mpp) REVERT: B 150 ARG cc_start: 0.8292 (mmt180) cc_final: 0.7175 (mtt-85) outliers start: 58 outliers final: 31 residues processed: 201 average time/residue: 0.1105 time to fit residues: 35.3706 Evaluate side-chains 183 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain L residue 92 HIS Chi-restraints excluded: chain L residue 126 CYS Chi-restraints excluded: chain L residue 131 GLU Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 189 HIS Chi-restraints excluded: chain L residue 300 SER Chi-restraints excluded: chain L residue 325 GLU Chi-restraints excluded: chain L residue 376 MET Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 183 LEU Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain N residue 399 MET Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 653 ARG Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain P residue 190 PHE Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain P residue 225 THR Chi-restraints excluded: chain P residue 239 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 193 optimal weight: 30.0000 chunk 83 optimal weight: 0.7980 chunk 132 optimal weight: 10.0000 chunk 84 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 154 optimal weight: 0.0270 chunk 169 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 19 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 overall best weight: 1.2440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 HIS N 18 ASN N 85 GLN ** P 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.107249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.088241 restraints weight = 63957.527| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 4.49 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16418 Z= 0.143 Angle : 0.614 11.454 22547 Z= 0.318 Chirality : 0.046 0.327 2519 Planarity : 0.004 0.046 2743 Dihedral : 18.351 175.448 2624 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.91 % Allowed : 20.22 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.20), residues: 1941 helix: 0.83 (0.26), residues: 415 sheet: -0.48 (0.24), residues: 441 loop : -0.73 (0.20), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 355 TYR 0.011 0.001 TYR N 32 PHE 0.015 0.001 PHE L 97 TRP 0.034 0.002 TRP C 499 HIS 0.007 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (16413) covalent geometry : angle 0.61226 / 0.32 (22537) SS BOND : bond 0.00528 / 0.28 ( 5) SS BOND : angle 2.02899 / 1.25 ( 10) hydrogen bonds : bond 0.04626 / 3.33 ( 564) hydrogen bonds : angle 5.39514 / 3.72 ( 1506) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 150 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8233 (mt) cc_final: 0.7854 (mt) REVERT: A 185 GLU cc_start: 0.6916 (mp0) cc_final: 0.6713 (mp0) REVERT: A 557 TYR cc_start: 0.7287 (OUTLIER) cc_final: 0.6712 (p90) REVERT: L 131 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8023 (tm-30) REVERT: L 148 TYR cc_start: 0.7442 (OUTLIER) cc_final: 0.7049 (p90) REVERT: L 189 HIS cc_start: 0.7823 (OUTLIER) cc_final: 0.6883 (t-90) REVERT: L 355 ARG cc_start: 0.8482 (mmm-85) cc_final: 0.8233 (mmt90) REVERT: N 133 MET cc_start: 0.6113 (tpp) cc_final: 0.5854 (tpp) REVERT: N 253 MET cc_start: 0.4898 (ptm) cc_final: 0.4509 (ppp) REVERT: C 134 MET cc_start: 0.8264 (ppp) cc_final: 0.7976 (ppp) REVERT: C 593 HIS cc_start: 0.8225 (m-70) cc_final: 0.8019 (t-90) REVERT: C 653 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7125 (mtm-85) REVERT: C 701 MET cc_start: 0.7814 (tpp) cc_final: 0.7535 (mpp) REVERT: B 150 ARG cc_start: 0.8349 (mmt180) cc_final: 0.7408 (mtt180) outliers start: 57 outliers final: 41 residues processed: 192 average time/residue: 0.1145 time to fit residues: 35.0117 Evaluate side-chains 189 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 143 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 557 TYR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain L residue 126 CYS Chi-restraints excluded: chain L residue 131 GLU Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 182 CYS Chi-restraints excluded: chain L residue 189 HIS Chi-restraints excluded: chain L residue 300 SER Chi-restraints excluded: chain L residue 320 LEU Chi-restraints excluded: chain L residue 324 CYS Chi-restraints excluded: chain L residue 325 GLU Chi-restraints excluded: chain L residue 376 MET Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 85 GLN Chi-restraints excluded: chain N residue 183 LEU Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain N residue 394 SER Chi-restraints excluded: chain N residue 398 ILE Chi-restraints excluded: chain N residue 399 MET Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 653 ARG Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain P residue 190 PHE Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain P residue 225 THR Chi-restraints excluded: chain P residue 239 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 78 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 175 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 504 GLN ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 HIS N 18 ASN ** N 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.107226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.088224 restraints weight = 63628.143| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 4.50 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16418 Z= 0.136 Angle : 0.612 11.999 22547 Z= 0.315 Chirality : 0.046 0.330 2519 Planarity : 0.004 0.046 2743 Dihedral : 18.299 175.397 2624 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.77 % Allowed : 21.11 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.20), residues: 1941 helix: 0.92 (0.26), residues: 409 sheet: -0.49 (0.24), residues: 439 loop : -0.71 (0.20), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 355 TYR 0.018 0.001 TYR L 154 PHE 0.019 0.001 PHE N 61 TRP 0.024 0.001 TRP C 499 HIS 0.006 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (16413) covalent geometry : angle 0.61057 / 0.31 (22537) SS BOND : bond 0.00270 / 0.14 ( 5) SS BOND : angle 2.04363 / 1.25 ( 10) hydrogen bonds : bond 0.04516 / 3.26 ( 564) hydrogen bonds : angle 5.28063 / 3.64 ( 1506) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 155 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8204 (mt) cc_final: 0.7864 (mt) REVERT: A 185 GLU cc_start: 0.6952 (mp0) cc_final: 0.6720 (mp0) REVERT: A 557 TYR cc_start: 0.7296 (OUTLIER) cc_final: 0.6727 (p90) REVERT: A 632 MET cc_start: 0.7757 (mmp) cc_final: 0.7360 (mmt) REVERT: L 131 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.6793 (tm-30) REVERT: L 133 ARG cc_start: 0.8667 (mmm-85) cc_final: 0.8321 (tpp-160) REVERT: L 148 TYR cc_start: 0.7389 (OUTLIER) cc_final: 0.7030 (p90) REVERT: L 189 HIS cc_start: 0.7812 (OUTLIER) cc_final: 0.6888 (t-90) REVERT: L 355 ARG cc_start: 0.8498 (mmm-85) cc_final: 0.8258 (mmt90) REVERT: N 59 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8887 (ptpp) REVERT: N 133 MET cc_start: 0.6192 (tpp) cc_final: 0.5961 (tpp) REVERT: N 253 MET cc_start: 0.5044 (ptm) cc_final: 0.4657 (ppp) REVERT: C 52 ARG cc_start: 0.6980 (mmp80) cc_final: 0.6720 (mmp80) REVERT: C 134 MET cc_start: 0.8261 (ppp) cc_final: 0.7923 (ppp) REVERT: C 574 TYR cc_start: 0.8708 (t80) cc_final: 0.8357 (t80) REVERT: C 701 MET cc_start: 0.7805 (tpp) cc_final: 0.7544 (mpp) REVERT: B 150 ARG cc_start: 0.8302 (mmt180) cc_final: 0.7497 (mtt180) outliers start: 55 outliers final: 37 residues processed: 193 average time/residue: 0.1170 time to fit residues: 35.2334 Evaluate side-chains 187 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 145 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 557 TYR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain L residue 131 GLU Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 189 HIS Chi-restraints excluded: chain L residue 300 SER Chi-restraints excluded: chain L residue 320 LEU Chi-restraints excluded: chain L residue 324 CYS Chi-restraints excluded: chain L residue 325 GLU Chi-restraints excluded: chain L residue 376 MET Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 183 LEU Chi-restraints excluded: chain N residue 194 LEU Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain N residue 394 SER Chi-restraints excluded: chain N residue 399 MET Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 653 ARG Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain P residue 190 PHE Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain P residue 221 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 33 optimal weight: 0.6980 chunk 195 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 64 optimal weight: 0.0770 chunk 158 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 98 optimal weight: 0.3980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 504 GLN ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 HIS N 18 ASN ** C 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.108091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.089214 restraints weight = 63422.744| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 4.47 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 16418 Z= 0.115 Angle : 0.607 12.298 22547 Z= 0.311 Chirality : 0.046 0.333 2519 Planarity : 0.004 0.044 2743 Dihedral : 18.227 175.534 2624 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.50 % Allowed : 22.00 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.20), residues: 1941 helix: 0.98 (0.27), residues: 409 sheet: -0.45 (0.24), residues: 433 loop : -0.68 (0.20), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 355 TYR 0.010 0.001 TYR N 21 PHE 0.016 0.001 PHE N 61 TRP 0.043 0.002 TRP C 499 HIS 0.006 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (16413) covalent geometry : angle 0.60591 / 0.31 (22537) SS BOND : bond 0.00244 / 0.12 ( 5) SS BOND : angle 1.99734 / 1.22 ( 10) hydrogen bonds : bond 0.04399 / 3.19 ( 564) hydrogen bonds : angle 5.19699 / 3.58 ( 1506) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 158 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8189 (mt) cc_final: 0.7871 (mt) REVERT: A 185 GLU cc_start: 0.6912 (mp0) cc_final: 0.6658 (mp0) REVERT: A 557 TYR cc_start: 0.7244 (OUTLIER) cc_final: 0.6644 (p90) REVERT: A 632 MET cc_start: 0.7757 (mmp) cc_final: 0.7545 (mmt) REVERT: L 131 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.6772 (tm-30) REVERT: L 133 ARG cc_start: 0.8673 (mmm-85) cc_final: 0.8328 (tpp-160) REVERT: L 148 TYR cc_start: 0.7208 (OUTLIER) cc_final: 0.6969 (p90) REVERT: L 189 HIS cc_start: 0.7719 (OUTLIER) cc_final: 0.6942 (t-90) REVERT: L 355 ARG cc_start: 0.8481 (mmm-85) cc_final: 0.8224 (mmt90) REVERT: L 360 GLN cc_start: 0.8066 (mp10) cc_final: 0.7773 (mp10) REVERT: N 59 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8855 (ptpp) REVERT: N 133 MET cc_start: 0.6158 (tpp) cc_final: 0.5919 (tpp) REVERT: N 253 MET cc_start: 0.5020 (ptm) cc_final: 0.4677 (ppp) REVERT: C 439 MET cc_start: 0.6510 (tmm) cc_final: 0.6168 (tmm) REVERT: C 574 TYR cc_start: 0.8694 (t80) cc_final: 0.8337 (t80) REVERT: C 593 HIS cc_start: 0.8262 (m-70) cc_final: 0.8057 (t-90) REVERT: C 701 MET cc_start: 0.7759 (tpp) cc_final: 0.7513 (tpp) REVERT: B 150 ARG cc_start: 0.8326 (mmt180) cc_final: 0.7499 (mtt180) outliers start: 51 outliers final: 38 residues processed: 192 average time/residue: 0.1202 time to fit residues: 36.3168 Evaluate side-chains 191 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 148 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 557 TYR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain L residue 131 GLU Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 189 HIS Chi-restraints excluded: chain L residue 300 SER Chi-restraints excluded: chain L residue 320 LEU Chi-restraints excluded: chain L residue 324 CYS Chi-restraints excluded: chain L residue 325 GLU Chi-restraints excluded: chain L residue 376 MET Chi-restraints excluded: chain N residue 36 MET Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 183 LEU Chi-restraints excluded: chain N residue 194 LEU Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain N residue 394 SER Chi-restraints excluded: chain N residue 399 MET Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 653 ARG Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain P residue 190 PHE Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain P residue 225 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 92 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 6 optimal weight: 30.0000 chunk 50 optimal weight: 0.8980 chunk 130 optimal weight: 9.9990 chunk 152 optimal weight: 8.9990 chunk 147 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 HIS N 18 ASN ** N 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.104860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.085898 restraints weight = 64101.413| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 4.40 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 16418 Z= 0.215 Angle : 0.671 12.767 22547 Z= 0.347 Chirality : 0.048 0.326 2519 Planarity : 0.004 0.047 2743 Dihedral : 18.279 174.982 2624 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.84 % Allowed : 22.00 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.19), residues: 1941 helix: 0.67 (0.26), residues: 414 sheet: -0.58 (0.24), residues: 426 loop : -0.88 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 52 TYR 0.020 0.002 TYR N 32 PHE 0.014 0.002 PHE P 222 TRP 0.058 0.002 TRP C 499 HIS 0.008 0.001 HIS L 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.22 (16413) covalent geometry : angle 0.66935 / 0.35 (22537) SS BOND : bond 0.01063 / 0.56 ( 5) SS BOND : angle 2.17061 / 1.35 ( 10) hydrogen bonds : bond 0.04829 / 3.46 ( 564) hydrogen bonds : angle 5.36953 / 3.71 ( 1506) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 149 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8298 (mt) cc_final: 0.7958 (mt) REVERT: A 185 GLU cc_start: 0.6986 (mp0) cc_final: 0.6641 (mp0) REVERT: A 557 TYR cc_start: 0.7204 (OUTLIER) cc_final: 0.6658 (p90) REVERT: L 100 GLN cc_start: 0.7790 (mt0) cc_final: 0.7267 (mt0) REVERT: L 131 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8071 (tm-30) REVERT: L 135 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7941 (mp) REVERT: N 59 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8903 (ptpp) REVERT: N 133 MET cc_start: 0.6203 (tpp) cc_final: 0.5994 (tpp) REVERT: N 253 MET cc_start: 0.5023 (ptm) cc_final: 0.4594 (ppp) REVERT: C 52 ARG cc_start: 0.7019 (mmp80) cc_final: 0.6777 (mmp80) REVERT: C 561 ARG cc_start: 0.6512 (tpt90) cc_final: 0.6248 (tpt90) REVERT: C 574 TYR cc_start: 0.8792 (t80) cc_final: 0.8468 (t80) REVERT: C 701 MET cc_start: 0.7908 (tpp) cc_final: 0.7598 (mpp) REVERT: B 150 ARG cc_start: 0.8463 (mmt180) cc_final: 0.8228 (mmt180) outliers start: 56 outliers final: 40 residues processed: 192 average time/residue: 0.1063 time to fit residues: 31.8218 Evaluate side-chains 191 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 557 TYR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain L residue 126 CYS Chi-restraints excluded: chain L residue 131 GLU Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 182 CYS Chi-restraints excluded: chain L residue 300 SER Chi-restraints excluded: chain L residue 324 CYS Chi-restraints excluded: chain L residue 325 GLU Chi-restraints excluded: chain L residue 376 MET Chi-restraints excluded: chain N residue 36 MET Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 183 LEU Chi-restraints excluded: chain N residue 194 LEU Chi-restraints excluded: chain N residue 226 HIS Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain N residue 339 ASP Chi-restraints excluded: chain N residue 394 SER Chi-restraints excluded: chain N residue 399 MET Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 653 ARG Chi-restraints excluded: chain P residue 190 PHE Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain P residue 225 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 139 optimal weight: 2.9990 chunk 146 optimal weight: 0.0770 chunk 162 optimal weight: 0.7980 chunk 176 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 33 optimal weight: 0.0470 chunk 24 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 42 optimal weight: 0.0970 chunk 195 optimal weight: 7.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.3634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 HIS N 18 ASN ** N 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 717 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.107352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.088389 restraints weight = 63036.739| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 4.49 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16418 Z= 0.120 Angle : 0.634 13.721 22547 Z= 0.323 Chirality : 0.047 0.338 2519 Planarity : 0.004 0.046 2743 Dihedral : 18.190 175.176 2624 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.22 % Allowed : 22.76 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.20), residues: 1941 helix: 0.85 (0.26), residues: 410 sheet: -0.57 (0.24), residues: 438 loop : -0.68 (0.20), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 355 TYR 0.012 0.001 TYR C 292 PHE 0.013 0.001 PHE L 97 TRP 0.069 0.002 TRP C 499 HIS 0.007 0.001 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (16413) covalent geometry : angle 0.63225 / 0.32 (22537) SS BOND : bond 0.00170 / 0.08 ( 5) SS BOND : angle 2.16842 / 1.34 ( 10) hydrogen bonds : bond 0.04417 / 3.20 ( 564) hydrogen bonds : angle 5.18930 / 3.58 ( 1506) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 157 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8245 (mt) cc_final: 0.7917 (mt) REVERT: A 185 GLU cc_start: 0.6991 (mp0) cc_final: 0.6673 (mp0) REVERT: A 557 TYR cc_start: 0.7096 (OUTLIER) cc_final: 0.6502 (p90) REVERT: L 131 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8059 (tm-30) REVERT: L 189 HIS cc_start: 0.7785 (OUTLIER) cc_final: 0.7261 (t-90) REVERT: L 314 TRP cc_start: 0.7160 (m-10) cc_final: 0.6663 (m-10) REVERT: N 59 LYS cc_start: 0.9136 (ptpp) cc_final: 0.8855 (ptpp) REVERT: N 133 MET cc_start: 0.6128 (tpp) cc_final: 0.5906 (tpp) REVERT: N 253 MET cc_start: 0.5110 (ptm) cc_final: 0.4590 (ppp) REVERT: C 439 MET cc_start: 0.6351 (tmm) cc_final: 0.6105 (tmm) REVERT: C 561 ARG cc_start: 0.6317 (tpt90) cc_final: 0.6028 (tpt90) REVERT: C 574 TYR cc_start: 0.8716 (t80) cc_final: 0.8423 (t80) REVERT: C 597 LYS cc_start: 0.6385 (OUTLIER) cc_final: 0.6023 (tptp) REVERT: C 701 MET cc_start: 0.7752 (tpp) cc_final: 0.7506 (tpp) REVERT: B 150 ARG cc_start: 0.8421 (mmt180) cc_final: 0.8175 (mmt180) outliers start: 47 outliers final: 34 residues processed: 192 average time/residue: 0.1144 time to fit residues: 34.0242 Evaluate side-chains 192 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 557 TYR Chi-restraints excluded: chain L residue 131 GLU Chi-restraints excluded: chain L residue 189 HIS Chi-restraints excluded: chain L residue 196 LEU Chi-restraints excluded: chain L residue 300 SER Chi-restraints excluded: chain L residue 324 CYS Chi-restraints excluded: chain L residue 325 GLU Chi-restraints excluded: chain N residue 36 MET Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 226 HIS Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain N residue 269 VAL Chi-restraints excluded: chain N residue 394 SER Chi-restraints excluded: chain N residue 399 MET Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 597 LYS Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 653 ARG Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain P residue 190 PHE Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain P residue 225 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 110 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 164 optimal weight: 0.7980 chunk 157 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 150 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 ASN ** N 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 717 GLN ** P 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.106880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.087949 restraints weight = 63708.050| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 4.47 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16418 Z= 0.129 Angle : 0.639 12.946 22547 Z= 0.325 Chirality : 0.047 0.331 2519 Planarity : 0.004 0.048 2743 Dihedral : 18.137 175.337 2624 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.81 % Allowed : 22.89 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.20), residues: 1941 helix: 0.81 (0.26), residues: 409 sheet: -0.50 (0.24), residues: 430 loop : -0.69 (0.20), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 355 TYR 0.021 0.001 TYR L 154 PHE 0.014 0.001 PHE L 97 TRP 0.076 0.002 TRP C 499 HIS 0.008 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (16413) covalent geometry : angle 0.63799 / 0.32 (22537) SS BOND : bond 0.00346 / 0.18 ( 5) SS BOND : angle 2.03763 / 1.27 ( 10) hydrogen bonds : bond 0.04498 / 3.23 ( 564) hydrogen bonds : angle 5.15742 / 3.57 ( 1506) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 157 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8278 (mt) cc_final: 0.7959 (mt) REVERT: A 185 GLU cc_start: 0.7013 (mp0) cc_final: 0.6677 (mp0) REVERT: A 557 TYR cc_start: 0.7134 (OUTLIER) cc_final: 0.6525 (p90) REVERT: L 100 GLN cc_start: 0.7769 (mt0) cc_final: 0.7275 (mt0) REVERT: L 131 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8028 (tm-30) REVERT: L 148 TYR cc_start: 0.7556 (OUTLIER) cc_final: 0.7025 (p90) REVERT: N 59 LYS cc_start: 0.9146 (ptpp) cc_final: 0.8854 (ptpp) REVERT: N 133 MET cc_start: 0.6128 (tpp) cc_final: 0.5916 (tpp) REVERT: N 253 MET cc_start: 0.5106 (ptm) cc_final: 0.4569 (ppp) REVERT: C 439 MET cc_start: 0.6418 (tmm) cc_final: 0.6122 (tmm) REVERT: C 561 ARG cc_start: 0.6187 (tpt90) cc_final: 0.5946 (tpt90) REVERT: C 574 TYR cc_start: 0.8687 (t80) cc_final: 0.8402 (t80) REVERT: C 597 LYS cc_start: 0.6424 (OUTLIER) cc_final: 0.6035 (tptp) REVERT: C 701 MET cc_start: 0.7757 (tpp) cc_final: 0.7503 (tpp) outliers start: 41 outliers final: 35 residues processed: 188 average time/residue: 0.1183 time to fit residues: 34.5761 Evaluate side-chains 192 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 557 TYR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain L residue 131 GLU Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 196 LEU Chi-restraints excluded: chain L residue 300 SER Chi-restraints excluded: chain L residue 324 CYS Chi-restraints excluded: chain L residue 325 GLU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 194 LEU Chi-restraints excluded: chain N residue 226 HIS Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain N residue 269 VAL Chi-restraints excluded: chain N residue 394 SER Chi-restraints excluded: chain N residue 399 MET Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 597 LYS Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 653 ARG Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain C residue 717 GLN Chi-restraints excluded: chain P residue 190 PHE Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain P residue 225 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 82 optimal weight: 4.9990 chunk 190 optimal weight: 0.5980 chunk 118 optimal weight: 40.0000 chunk 91 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.105175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.086254 restraints weight = 63658.155| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 4.43 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 16418 Z= 0.207 Angle : 0.691 14.194 22547 Z= 0.355 Chirality : 0.048 0.328 2519 Planarity : 0.005 0.072 2743 Dihedral : 18.179 175.021 2624 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 3.15 % Allowed : 22.89 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.19), residues: 1941 helix: 0.64 (0.26), residues: 408 sheet: -0.60 (0.24), residues: 432 loop : -0.74 (0.20), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 355 TYR 0.031 0.002 TYR L 308 PHE 0.014 0.002 PHE C 120 TRP 0.096 0.003 TRP C 499 HIS 0.008 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.21 (16413) covalent geometry : angle 0.68968 / 0.35 (22537) SS BOND : bond 0.00447 / 0.24 ( 5) SS BOND : angle 2.18261 / 1.36 ( 10) hydrogen bonds : bond 0.04782 / 3.40 ( 564) hydrogen bonds : angle 5.28838 / 3.67 ( 1506) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4084.56 seconds wall clock time: 71 minutes 3.52 seconds (4263.52 seconds total)