Starting phenix.real_space_refine on Thu Sep 18 13:32:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vnv_43361/09_2025/8vnv_43361.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vnv_43361/09_2025/8vnv_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_43361/09_2025/8vnv_43361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vnv_43361/09_2025/8vnv_43361.map" model { file = "/net/cci-nas-00/data/ceres_data/8vnv_43361/09_2025/8vnv_43361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vnv_43361/09_2025/8vnv_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-2.0-5805/lib/python3.9/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: 4.63, per 1000 atoms: 0.29 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: 1.82 Conformation dependent library (CDL) restraints added in 764.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.17 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: 3.54 Time building geometry restraints manager: 2.28 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=" 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=" C8 SAH C 801 " pdb=" N7 SAH C 801 " ideal model delta sigma weight residual 1.299 1.349 -0.050 2.00e-02 2.50e+03 6.35e+00 bond pdb=" C2 SAH C 801 " pdb=" N1 SAH C 801 " ideal model delta sigma weight residual 1.330 1.380 -0.050 2.00e-02 2.50e+03 6.29e+00 bond pdb=" C6 SAH C 801 " pdb=" N1 SAH C 801 " ideal model delta sigma weight residual 1.338 1.379 -0.041 2.00e-02 2.50e+03 4.19e+00 bond pdb=" C3' DG D 161 " pdb=" O3' DG D 161 " ideal model delta sigma weight residual 1.422 1.474 -0.052 3.00e-02 1.11e+03 3.00e+00 ... (remaining 16408 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 22051 2.07 - 4.15: 413 4.15 - 6.22: 54 6.22 - 8.30: 11 8.30 - 10.37: 8 Bond angle restraints: 22537 Sorted by residual: 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=" CA LYS P 231 " pdb=" CB LYS P 231 " pdb=" CG LYS P 231 " ideal model delta sigma weight residual 114.10 122.51 -8.41 2.00e+00 2.50e-01 1.77e+01 angle pdb=" N TYR L 148 " pdb=" CA TYR L 148 " pdb=" C TYR L 148 " ideal model delta sigma weight residual 107.60 114.67 -7.07 1.83e+00 2.99e-01 1.49e+01 angle pdb=" CG SAH C 801 " pdb=" SD SAH C 801 " pdb=" C5' SAH C 801 " ideal model delta sigma weight residual 101.77 91.40 10.37 3.00e+00 1.11e-01 1.19e+01 angle pdb=" N ASN N 277 " pdb=" CA ASN N 277 " pdb=" C ASN N 277 " ideal model delta sigma weight residual 107.32 113.02 -5.70 1.65e+00 3.67e-01 1.19e+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: 2051 0.053 - 0.105: 385 0.105 - 0.158: 81 0.158 - 0.210: 1 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=" CB VAL N 210 " pdb=" CA VAL N 210 " pdb=" CG1 VAL N 210 " pdb=" CG2 VAL N 210 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.35e-01 chirality pdb=" CA VAL L 209 " pdb=" N VAL L 209 " pdb=" C VAL L 209 " pdb=" CB VAL L 209 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.99e-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: 6.770 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: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.650 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.010 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:1.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 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= 0.148 Angle : 0.685 10.369 22547 Z= 0.364 Chirality : 0.043 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 aren 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 covalent geometry : bond 0.00316 (16413) covalent geometry : angle 0.68324 (22537) SS BOND : bond 0.00345 ( 5) SS BOND : angle 2.46990 ( 10) hydrogen bonds : bond 0.21581 ( 564) hydrogen bonds : angle 7.73986 ( 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 : 0.625 Fit side-chains revert: symmetry clash REVERT: A 632 MET cc_start: 0.7257 (mmt) cc_final: 0.6871 (mmt) outliers start: 7 outliers final: 2 residues processed: 163 average time/residue: 0.1315 time to fit residues: 33.0702 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 : 0.685 ------------------------------------------------------------------------------- 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: 7.9990 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... Flipped N/Q/H residues before XYZ refinement: ** 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 193 GLN ** P 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.110215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.091502 restraints weight = 63158.589| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 4.60 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16418 Z= 0.127 Angle : 0.603 8.813 22547 Z= 0.315 Chirality : 0.044 0.192 2519 Planarity : 0.004 0.052 2743 Dihedral : 18.363 176.015 2627 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.81 % Allowed : 19.19 % Favored : 78.00 % 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 aren not related in a simple way. whole: -0.31 (0.19), residues: 1941 helix: 0.84 (0.26), residues: 413 sheet: -0.00 (0.24), residues: 434 loop : -0.67 (0.20), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 355 TYR 0.012 0.001 TYR A 557 PHE 0.019 0.001 PHE C 290 TRP 0.019 0.001 TRP L 314 HIS 0.005 0.001 HIS N 236 Details of bonding type rmsd covalent geometry : bond 0.00280 (16413) covalent geometry : angle 0.60185 (22537) SS BOND : bond 0.00248 ( 5) SS BOND : angle 2.10003 ( 10) hydrogen bonds : bond 0.04890 ( 564) hydrogen bonds : angle 5.82455 ( 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 208 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 167 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8226 (mt) cc_final: 0.7951 (mt) REVERT: A 118 MET cc_start: 0.5908 (mmm) cc_final: 0.5622 (mmm) REVERT: A 184 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7284 (tt) REVERT: A 637 MET cc_start: 0.8532 (mtp) cc_final: 0.8289 (mtt) REVERT: L 189 HIS cc_start: 0.7736 (OUTLIER) cc_final: 0.6828 (t-90) REVERT: L 366 MET cc_start: 0.6407 (mtm) cc_final: 0.6099 (mtm) REVERT: N 133 MET cc_start: 0.6104 (tpp) cc_final: 0.5897 (tpp) REVERT: C 439 MET cc_start: 0.6826 (tmm) cc_final: 0.6389 (tmm) REVERT: C 701 MET cc_start: 0.7528 (tpp) cc_final: 0.7309 (mpp) outliers start: 41 outliers final: 21 residues processed: 198 average time/residue: 0.1235 time to fit residues: 38.0715 Evaluate side-chains 172 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 182 CYS 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 320 LEU 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 220 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 29 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 157 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 131 optimal weight: 8.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 ASN ** P 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.107030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.088184 restraints weight = 64412.015| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 4.51 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16418 Z= 0.149 Angle : 0.604 11.044 22547 Z= 0.314 Chirality : 0.044 0.163 2519 Planarity : 0.004 0.050 2743 Dihedral : 18.261 175.941 2624 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.04 % Allowed : 18.92 % Favored : 77.04 % 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 aren not related in a simple way. whole: -0.40 (0.19), residues: 1941 helix: 0.79 (0.26), residues: 414 sheet: -0.17 (0.25), residues: 427 loop : -0.68 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 355 TYR 0.015 0.001 TYR L 154 PHE 0.016 0.001 PHE L 97 TRP 0.030 0.002 TRP C 499 HIS 0.006 0.001 HIS C 297 Details of bonding type rmsd covalent geometry : bond 0.00342 (16413) covalent geometry : angle 0.60267 (22537) SS BOND : bond 0.00531 ( 5) SS BOND : angle 1.95111 ( 10) hydrogen bonds : bond 0.04658 ( 564) hydrogen bonds : angle 5.43931 ( 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 220 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 161 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8225 (mt) cc_final: 0.7973 (mt) REVERT: A 637 MET cc_start: 0.8603 (mtp) cc_final: 0.8367 (mtt) REVERT: L 131 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8046 (tm-30) REVERT: L 148 TYR cc_start: 0.7349 (OUTLIER) cc_final: 0.6891 (p90) REVERT: L 189 HIS cc_start: 0.7848 (OUTLIER) cc_final: 0.6890 (t-90) REVERT: L 366 MET cc_start: 0.6508 (mtm) cc_final: 0.6160 (mtm) REVERT: L 388 VAL cc_start: 0.8883 (t) cc_final: 0.8625 (p) REVERT: N 133 MET cc_start: 0.6121 (tpp) cc_final: 0.5867 (tpp) REVERT: C 52 ARG cc_start: 0.6946 (mmp80) cc_final: 0.6742 (mmp80) REVERT: C 134 MET cc_start: 0.8301 (ppp) cc_final: 0.7981 (ppp) REVERT: C 439 MET cc_start: 0.6876 (tmm) cc_final: 0.6672 (tmm) REVERT: C 701 MET cc_start: 0.7610 (tpp) cc_final: 0.7321 (mpp) outliers start: 59 outliers final: 29 residues processed: 208 average time/residue: 0.1195 time to fit residues: 38.5181 Evaluate side-chains 183 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 179 THR Chi-restraints excluded: chain L residue 182 CYS Chi-restraints excluded: chain L residue 189 HIS Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 300 SER Chi-restraints excluded: chain L residue 324 CYS Chi-restraints excluded: chain L residue 376 MET Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 80 VAL 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 632 VAL Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain C residue 729 SER Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain P residue 226 VAL Chi-restraints excluded: chain P residue 239 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 198 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 145 optimal weight: 0.0570 chunk 75 optimal weight: 10.0000 chunk 162 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 chunk 188 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 158 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 HIS N 18 ASN ** C 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN I 39 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.108269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.089549 restraints weight = 63759.611| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 4.50 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16418 Z= 0.120 Angle : 0.582 11.894 22547 Z= 0.301 Chirality : 0.043 0.183 2519 Planarity : 0.004 0.047 2743 Dihedral : 18.158 175.941 2624 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.43 % Allowed : 20.15 % Favored : 76.42 % 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 aren not related in a simple way. whole: -0.29 (0.20), residues: 1941 helix: 0.98 (0.27), residues: 410 sheet: -0.21 (0.24), residues: 434 loop : -0.60 (0.20), residues: 1097 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 0.012 0.001 PHE L 97 TRP 0.028 0.001 TRP L 314 HIS 0.005 0.001 HIS C 297 Details of bonding type rmsd covalent geometry : bond 0.00273 (16413) covalent geometry : angle 0.58046 (22537) SS BOND : bond 0.00234 ( 5) SS BOND : angle 1.95797 ( 10) hydrogen bonds : bond 0.04345 ( 564) hydrogen bonds : angle 5.16069 ( 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 216 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 166 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8188 (mt) cc_final: 0.7908 (mt) REVERT: L 131 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8000 (tm-30) REVERT: L 148 TYR cc_start: 0.7223 (OUTLIER) cc_final: 0.6917 (p90) REVERT: L 189 HIS cc_start: 0.7776 (OUTLIER) cc_final: 0.6945 (t-90) REVERT: L 355 ARG cc_start: 0.8546 (mmm-85) cc_final: 0.8264 (mmt90) REVERT: L 366 MET cc_start: 0.6500 (mtm) cc_final: 0.6168 (mtm) REVERT: N 32 TYR cc_start: 0.7998 (m-80) cc_final: 0.7743 (m-80) REVERT: N 133 MET cc_start: 0.6158 (tpp) cc_final: 0.5882 (tpp) REVERT: C 52 ARG cc_start: 0.6986 (mmp80) cc_final: 0.6754 (mmp80) REVERT: C 134 MET cc_start: 0.8253 (ppp) cc_final: 0.7856 (ppp) REVERT: C 701 MET cc_start: 0.7672 (tpp) cc_final: 0.7409 (mpp) outliers start: 50 outliers final: 30 residues processed: 205 average time/residue: 0.1110 time to fit residues: 35.8156 Evaluate side-chains 184 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 600 ILE Chi-restraints excluded: chain L residue 131 GLU Chi-restraints excluded: chain L residue 148 TYR 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 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 37 THR Chi-restraints excluded: chain N residue 80 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 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 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: 10.0000 chunk 83 optimal weight: 0.6980 chunk 132 optimal weight: 20.0000 chunk 84 optimal weight: 0.1980 chunk 109 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN ** 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 ** P 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.105822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.086770 restraints weight = 63526.959| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 4.44 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 16418 Z= 0.170 Angle : 0.614 12.897 22547 Z= 0.320 Chirality : 0.044 0.202 2519 Planarity : 0.004 0.050 2743 Dihedral : 18.142 175.341 2624 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.63 % Allowed : 21.45 % Favored : 74.91 % 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 aren not related in a simple way. whole: -0.40 (0.20), residues: 1941 helix: 0.89 (0.26), residues: 409 sheet: -0.17 (0.25), residues: 416 loop : -0.72 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 355 TYR 0.016 0.001 TYR N 32 PHE 0.014 0.002 PHE N 61 TRP 0.036 0.002 TRP C 499 HIS 0.006 0.001 HIS C 297 Details of bonding type rmsd covalent geometry : bond 0.00396 (16413) covalent geometry : angle 0.61261 (22537) SS BOND : bond 0.00098 ( 5) SS BOND : angle 2.09922 ( 10) hydrogen bonds : bond 0.04582 ( 564) hydrogen bonds : angle 5.25954 ( 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 213 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 160 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8203 (mt) cc_final: 0.7966 (mt) REVERT: A 198 ASP cc_start: 0.8086 (m-30) cc_final: 0.7545 (p0) REVERT: A 557 TYR cc_start: 0.7059 (OUTLIER) cc_final: 0.6522 (p90) REVERT: L 100 GLN cc_start: 0.7647 (mt0) cc_final: 0.7159 (mt0) REVERT: L 131 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8123 (tm-30) REVERT: L 135 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7916 (mp) REVERT: L 366 MET cc_start: 0.6695 (mtm) cc_final: 0.6325 (mtm) REVERT: N 133 MET cc_start: 0.6144 (tpp) cc_final: 0.5895 (tpp) REVERT: N 360 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8429 (pt0) REVERT: C 134 MET cc_start: 0.8352 (ppp) cc_final: 0.7945 (ppp) REVERT: C 561 ARG cc_start: 0.6423 (tpt90) cc_final: 0.6128 (tpt90) REVERT: C 574 TYR cc_start: 0.8708 (t80) cc_final: 0.8314 (t80) REVERT: C 597 LYS cc_start: 0.6405 (OUTLIER) cc_final: 0.5990 (tptp) REVERT: C 701 MET cc_start: 0.7835 (tpp) cc_final: 0.7544 (mpp) outliers start: 53 outliers final: 36 residues processed: 201 average time/residue: 0.1198 time to fit residues: 37.1657 Evaluate side-chains 192 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 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 92 HIS Chi-restraints excluded: chain L residue 131 GLU Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 182 CYS 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 L residue 376 MET Chi-restraints excluded: chain L residue 434 ILE 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 252 LEU Chi-restraints excluded: chain N residue 360 GLU 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 593 HIS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 78 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 162 optimal weight: 0.0010 chunk 62 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 112 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.106648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.087655 restraints weight = 62995.155| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 4.49 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16418 Z= 0.128 Angle : 0.592 13.383 22547 Z= 0.305 Chirality : 0.043 0.194 2519 Planarity : 0.004 0.047 2743 Dihedral : 18.058 174.990 2624 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.98 % Allowed : 21.32 % Favored : 74.71 % 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 aren not related in a simple way. whole: -0.32 (0.20), residues: 1941 helix: 0.99 (0.27), residues: 408 sheet: -0.31 (0.25), residues: 433 loop : -0.59 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 355 TYR 0.029 0.001 TYR L 308 PHE 0.019 0.001 PHE N 61 TRP 0.036 0.001 TRP L 314 HIS 0.007 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00293 (16413) covalent geometry : angle 0.59054 (22537) SS BOND : bond 0.00288 ( 5) SS BOND : angle 2.03029 ( 10) hydrogen bonds : bond 0.04338 ( 564) hydrogen bonds : angle 5.11775 ( 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 219 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 161 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8146 (mt) cc_final: 0.7898 (mt) REVERT: A 557 TYR cc_start: 0.7115 (OUTLIER) cc_final: 0.6546 (p90) REVERT: L 131 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8108 (tm-30) REVERT: L 148 TYR cc_start: 0.7562 (OUTLIER) cc_final: 0.7030 (p90) REVERT: L 189 HIS cc_start: 0.7850 (OUTLIER) cc_final: 0.6930 (t-90) REVERT: L 366 MET cc_start: 0.6716 (mtm) cc_final: 0.6343 (mtm) REVERT: N 118 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7916 (tm-30) REVERT: N 133 MET cc_start: 0.6096 (tpp) cc_final: 0.5861 (tpp) REVERT: N 253 MET cc_start: 0.4634 (ptm) cc_final: 0.3346 (ppp) REVERT: C 574 TYR cc_start: 0.8674 (t80) cc_final: 0.8323 (t80) REVERT: C 597 LYS cc_start: 0.6412 (OUTLIER) cc_final: 0.6030 (tptp) REVERT: C 701 MET cc_start: 0.7773 (tpp) cc_final: 0.7521 (tpp) outliers start: 58 outliers final: 38 residues processed: 204 average time/residue: 0.1244 time to fit residues: 39.2238 Evaluate side-chains 201 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 157 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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 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 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 92 HIS Chi-restraints excluded: chain L residue 131 GLU Chi-restraints excluded: chain L residue 148 TYR 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 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 37 THR Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 118 GLU 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 593 HIS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 33 optimal weight: 4.9990 chunk 195 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 8 optimal weight: 20.0000 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.105299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.086472 restraints weight = 63101.864| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 4.44 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16418 Z= 0.160 Angle : 0.621 13.482 22547 Z= 0.319 Chirality : 0.044 0.223 2519 Planarity : 0.004 0.048 2743 Dihedral : 18.034 174.626 2624 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 4.04 % Allowed : 22.07 % Favored : 73.89 % 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 aren not related in a simple way. whole: -0.41 (0.20), residues: 1941 helix: 0.93 (0.26), residues: 410 sheet: -0.34 (0.25), residues: 425 loop : -0.67 (0.20), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 355 TYR 0.018 0.001 TYR L 154 PHE 0.016 0.001 PHE A 161 TRP 0.026 0.002 TRP L 314 HIS 0.007 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00367 (16413) covalent geometry : angle 0.61923 (22537) SS BOND : bond 0.00114 ( 5) SS BOND : angle 2.16107 ( 10) hydrogen bonds : bond 0.04463 ( 564) hydrogen bonds : angle 5.13733 ( 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 215 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 156 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8192 (mt) cc_final: 0.7937 (mt) REVERT: A 198 ASP cc_start: 0.8056 (m-30) cc_final: 0.7510 (p0) REVERT: A 557 TYR cc_start: 0.7062 (OUTLIER) cc_final: 0.6492 (p90) REVERT: L 100 GLN cc_start: 0.7688 (mt0) cc_final: 0.7186 (mt0) REVERT: L 131 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8138 (tm-30) REVERT: L 148 TYR cc_start: 0.7593 (OUTLIER) cc_final: 0.6981 (p90) REVERT: L 189 HIS cc_start: 0.7917 (OUTLIER) cc_final: 0.6922 (t-90) REVERT: L 337 GLU cc_start: 0.9013 (pm20) cc_final: 0.8785 (mp0) REVERT: N 118 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7911 (tm-30) REVERT: N 133 MET cc_start: 0.6126 (tpp) cc_final: 0.5899 (tpp) REVERT: N 253 MET cc_start: 0.4549 (ptm) cc_final: 0.3654 (ppp) REVERT: N 360 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8422 (pt0) REVERT: C 561 ARG cc_start: 0.6377 (tpt90) cc_final: 0.6059 (tpt90) REVERT: C 574 TYR cc_start: 0.8705 (t80) cc_final: 0.8364 (t80) REVERT: C 701 MET cc_start: 0.7836 (tpp) cc_final: 0.7538 (mpp) REVERT: P 259 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7485 (mmm160) outliers start: 59 outliers final: 42 residues processed: 204 average time/residue: 0.1277 time to fit residues: 39.7903 Evaluate side-chains 195 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 146 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 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 507 HIS Chi-restraints excluded: chain A residue 514 PHE 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 179 THR Chi-restraints excluded: chain L residue 182 CYS 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 L residue 376 MET 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 118 GLU Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain N residue 269 VAL Chi-restraints excluded: chain N residue 339 ASP Chi-restraints excluded: chain N residue 360 GLU Chi-restraints excluded: chain N residue 394 SER Chi-restraints excluded: chain N residue 399 MET Chi-restraints excluded: chain N residue 410 ASN 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 593 HIS Chi-restraints excluded: chain C residue 628 ILE 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 225 THR Chi-restraints excluded: chain P residue 259 ARG 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: 6.9990 chunk 175 optimal weight: 3.9990 chunk 6 optimal weight: 40.0000 chunk 50 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 ASN N 85 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 = 0.4265 r_free = 0.4265 target = 0.104635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.085714 restraints weight = 63207.804| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 4.45 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16418 Z= 0.179 Angle : 0.646 13.806 22547 Z= 0.332 Chirality : 0.044 0.221 2519 Planarity : 0.004 0.048 2743 Dihedral : 18.027 174.375 2624 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 4.46 % Allowed : 21.86 % Favored : 73.68 % 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 aren not related in a simple way. whole: -0.51 (0.20), residues: 1941 helix: 0.89 (0.26), residues: 410 sheet: -0.42 (0.25), residues: 426 loop : -0.74 (0.20), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 355 TYR 0.016 0.001 TYR N 32 PHE 0.013 0.002 PHE L 97 TRP 0.050 0.002 TRP C 499 HIS 0.007 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00410 (16413) covalent geometry : angle 0.64410 (22537) SS BOND : bond 0.00388 ( 5) SS BOND : angle 2.16775 ( 10) hydrogen bonds : bond 0.04553 ( 564) hydrogen bonds : angle 5.22004 ( 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 210 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 145 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8180 (mt) cc_final: 0.7964 (mt) REVERT: A 557 TYR cc_start: 0.7035 (OUTLIER) cc_final: 0.6505 (p90) REVERT: L 100 GLN cc_start: 0.7716 (mt0) cc_final: 0.7222 (mt0) REVERT: L 131 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8143 (tm-30) REVERT: L 148 TYR cc_start: 0.7577 (OUTLIER) cc_final: 0.7033 (p90) REVERT: L 189 HIS cc_start: 0.7952 (OUTLIER) cc_final: 0.6931 (t-90) REVERT: L 337 GLU cc_start: 0.9028 (pm20) cc_final: 0.8799 (mp0) REVERT: N 118 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7940 (tm-30) REVERT: N 133 MET cc_start: 0.6144 (tpp) cc_final: 0.5936 (tpp) REVERT: N 253 MET cc_start: 0.4272 (ptm) cc_final: 0.3488 (ppp) REVERT: C 439 MET cc_start: 0.6538 (tmm) cc_final: 0.6202 (tmm) REVERT: C 561 ARG cc_start: 0.6481 (tpt90) cc_final: 0.6259 (tpt90) REVERT: C 574 TYR cc_start: 0.8710 (t80) cc_final: 0.8392 (t80) REVERT: P 259 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7523 (mmm160) outliers start: 65 outliers final: 44 residues processed: 197 average time/residue: 0.1250 time to fit residues: 37.8704 Evaluate side-chains 192 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 142 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 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 514 PHE 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 179 THR Chi-restraints excluded: chain L residue 182 CYS 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 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 434 ILE 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 118 GLU Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain N residue 269 VAL 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 N residue 410 ASN 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 593 HIS Chi-restraints excluded: chain C residue 628 ILE 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 221 VAL Chi-restraints excluded: chain P residue 225 THR Chi-restraints excluded: chain P residue 259 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 139 optimal weight: 6.9990 chunk 146 optimal weight: 0.0050 chunk 162 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 195 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 ASN N 85 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 = 0.4266 r_free = 0.4266 target = 0.104672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.085751 restraints weight = 62792.759| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 4.43 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16418 Z= 0.169 Angle : 0.645 14.048 22547 Z= 0.332 Chirality : 0.044 0.306 2519 Planarity : 0.004 0.047 2743 Dihedral : 18.001 174.042 2624 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 4.11 % Allowed : 22.00 % Favored : 73.89 % 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 aren not related in a simple way. whole: -0.54 (0.20), residues: 1941 helix: 0.91 (0.26), residues: 409 sheet: -0.53 (0.24), residues: 431 loop : -0.74 (0.20), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 355 TYR 0.015 0.001 TYR N 32 PHE 0.012 0.001 PHE L 97 TRP 0.055 0.002 TRP C 499 HIS 0.008 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00388 (16413) covalent geometry : angle 0.64368 (22537) SS BOND : bond 0.00387 ( 5) SS BOND : angle 2.35104 ( 10) hydrogen bonds : bond 0.04546 ( 564) hydrogen bonds : angle 5.20652 ( 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 210 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 150 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8156 (mt) cc_final: 0.7940 (mt) REVERT: A 198 ASP cc_start: 0.8079 (m-30) cc_final: 0.7467 (p0) REVERT: A 557 TYR cc_start: 0.7117 (OUTLIER) cc_final: 0.6584 (p90) REVERT: L 100 GLN cc_start: 0.7748 (mt0) cc_final: 0.7254 (mt0) REVERT: L 131 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8112 (tm-30) REVERT: L 135 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7881 (mp) REVERT: L 148 TYR cc_start: 0.7476 (OUTLIER) cc_final: 0.7136 (p90) REVERT: L 189 HIS cc_start: 0.7933 (OUTLIER) cc_final: 0.6880 (t-90) REVERT: L 314 TRP cc_start: 0.6993 (m-10) cc_final: 0.6728 (m-10) REVERT: L 337 GLU cc_start: 0.9037 (pm20) cc_final: 0.8790 (mp0) REVERT: N 118 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7944 (tm-30) REVERT: N 133 MET cc_start: 0.6126 (tpp) cc_final: 0.5923 (tpp) REVERT: N 253 MET cc_start: 0.4312 (ptm) cc_final: 0.3585 (ppp) REVERT: N 360 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7956 (pt0) REVERT: C 502 HIS cc_start: 0.8695 (m90) cc_final: 0.8483 (m90) REVERT: C 561 ARG cc_start: 0.6550 (tpt90) cc_final: 0.6332 (tpt90) REVERT: C 574 TYR cc_start: 0.8686 (t80) cc_final: 0.8352 (t80) REVERT: P 259 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7547 (mmm160) outliers start: 60 outliers final: 43 residues processed: 195 average time/residue: 0.1075 time to fit residues: 32.6261 Evaluate side-chains 195 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 144 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 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 514 PHE 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 135 LEU Chi-restraints excluded: chain L residue 148 TYR 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 196 LEU 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 434 ILE 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 118 GLU Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain N residue 269 VAL Chi-restraints excluded: chain N residue 339 ASP Chi-restraints excluded: chain N residue 360 GLU Chi-restraints excluded: chain N residue 394 SER Chi-restraints excluded: chain N residue 399 MET Chi-restraints excluded: chain N residue 410 ASN 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 593 HIS Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain C residue 729 SER 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 259 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 110 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 135 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 HIS N 18 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.105906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.087099 restraints weight = 62798.298| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 4.47 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16418 Z= 0.135 Angle : 0.631 13.780 22547 Z= 0.322 Chirality : 0.044 0.292 2519 Planarity : 0.004 0.046 2743 Dihedral : 17.931 173.959 2624 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.50 % Allowed : 22.41 % Favored : 74.09 % 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 aren not related in a simple way. whole: -0.48 (0.20), residues: 1941 helix: 0.91 (0.26), residues: 410 sheet: -0.46 (0.25), residues: 430 loop : -0.69 (0.20), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 355 TYR 0.012 0.001 TYR C 448 PHE 0.011 0.001 PHE L 97 TRP 0.062 0.002 TRP C 499 HIS 0.008 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00311 (16413) covalent geometry : angle 0.62967 (22537) SS BOND : bond 0.00346 ( 5) SS BOND : angle 2.15607 ( 10) hydrogen bonds : bond 0.04417 ( 564) hydrogen bonds : angle 5.11746 ( 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 208 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 157 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8113 (mt) cc_final: 0.7895 (mt) REVERT: A 557 TYR cc_start: 0.7179 (OUTLIER) cc_final: 0.6590 (p90) REVERT: L 100 GLN cc_start: 0.7721 (mt0) cc_final: 0.7276 (mt0) REVERT: L 131 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8103 (tm-30) REVERT: L 135 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7751 (mp) REVERT: L 148 TYR cc_start: 0.7502 (OUTLIER) cc_final: 0.7172 (p90) REVERT: L 189 HIS cc_start: 0.7871 (OUTLIER) cc_final: 0.7034 (t-90) REVERT: L 337 GLU cc_start: 0.8989 (pm20) cc_final: 0.8740 (mp0) REVERT: N 118 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7957 (tm-30) REVERT: N 133 MET cc_start: 0.6111 (tpp) cc_final: 0.5894 (tpp) REVERT: N 253 MET cc_start: 0.3945 (ptm) cc_final: 0.3718 (ppp) REVERT: N 360 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7947 (pt0) REVERT: C 439 MET cc_start: 0.6282 (tmm) cc_final: 0.6032 (tmm) REVERT: C 502 HIS cc_start: 0.8636 (m90) cc_final: 0.8432 (m90) REVERT: C 561 ARG cc_start: 0.6414 (tpt90) cc_final: 0.6110 (tpt90) REVERT: C 574 TYR cc_start: 0.8609 (t80) cc_final: 0.8283 (t80) REVERT: C 579 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7149 (tp30) REVERT: P 259 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7468 (mmm160) outliers start: 51 outliers final: 40 residues processed: 197 average time/residue: 0.1301 time to fit residues: 38.7885 Evaluate side-chains 200 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 152 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 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 514 PHE 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 135 LEU Chi-restraints excluded: chain L residue 148 TYR 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 196 LEU Chi-restraints excluded: chain L residue 320 LEU Chi-restraints excluded: chain L residue 322 LYS 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 37 THR Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 118 GLU Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 230 VAL Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain N residue 269 VAL Chi-restraints excluded: chain N residue 339 ASP Chi-restraints excluded: chain N residue 360 GLU Chi-restraints excluded: chain N residue 394 SER 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 593 HIS Chi-restraints excluded: chain C residue 628 ILE 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 225 THR Chi-restraints excluded: chain P residue 259 ARG 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: 7.9990 chunk 118 optimal weight: 30.0000 chunk 91 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 27 optimal weight: 0.0770 chunk 54 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 ASN N 85 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.104921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.086003 restraints weight = 62735.348| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 4.48 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16418 Z= 0.152 Angle : 0.638 13.749 22547 Z= 0.327 Chirality : 0.044 0.286 2519 Planarity : 0.004 0.047 2743 Dihedral : 17.908 174.359 2624 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 3.56 % Allowed : 22.28 % 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 aren not related in a simple way. whole: -0.55 (0.20), residues: 1941 helix: 0.88 (0.26), residues: 408 sheet: -0.58 (0.25), residues: 425 loop : -0.72 (0.20), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 355 TYR 0.013 0.001 TYR C 448 PHE 0.012 0.001 PHE L 97 TRP 0.067 0.002 TRP C 499 HIS 0.008 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00350 (16413) covalent geometry : angle 0.63604 (22537) SS BOND : bond 0.00347 ( 5) SS BOND : angle 2.20807 ( 10) hydrogen bonds : bond 0.04479 ( 564) hydrogen bonds : angle 5.13254 ( 1506) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4193.53 seconds wall clock time: 72 minutes 53.97 seconds (4373.97 seconds total)