Starting phenix.real_space_refine on Thu Sep 18 03:52:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kbh_62225/09_2025/9kbh_62225.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kbh_62225/09_2025/9kbh_62225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kbh_62225/09_2025/9kbh_62225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kbh_62225/09_2025/9kbh_62225.map" model { file = "/net/cci-nas-00/data/ceres_data/9kbh_62225/09_2025/9kbh_62225.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kbh_62225/09_2025/9kbh_62225.cif" } resolution = 3.3 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= -0.001 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 23 5.49 5 Mg 4 5.21 5 S 73 5.16 5 C 8801 2.51 5 N 2306 2.21 5 O 2556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 13763 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2213 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 13, 'TRANS': 276} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 2285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2285 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 13, 'TRANS': 280} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 2285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2285 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 13, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2285 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 13, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2282 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 13, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 2105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2105 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 11, 'TRANS': 265} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 3, 'PHE:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "H" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 122 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.35, per 1000 atoms: 0.24 Number of scatterers: 13763 At special positions: 0 Unit cell: (87.269, 134.26, 125.629, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 73 16.00 P 23 15.00 Mg 4 11.99 O 2556 8.00 N 2306 7.00 C 8801 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 631.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 13 sheets defined 48.6% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 210 through 226 Processing helix chain 'A' and resid 230 through 238 Processing helix chain 'A' and resid 238 through 246 removed outlier: 4.023A pdb=" N TYR A 242 " --> pdb=" O ASP A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 270 removed outlier: 3.501A pdb=" N GLN A 254 " --> pdb=" O SER A 250 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLN A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 257 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 removed outlier: 3.838A pdb=" N PHE A 275 " --> pdb=" O PRO A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 299 Processing helix chain 'A' and resid 302 through 315 removed outlier: 3.981A pdb=" N ASP A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 343 removed outlier: 3.689A pdb=" N ALA A 338 " --> pdb=" O LYS A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 382 removed outlier: 4.225A pdb=" N GLU A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 390 removed outlier: 4.391A pdb=" N ALA A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 437 removed outlier: 3.568A pdb=" N LEU A 435 " --> pdb=" O HIS A 431 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU A 437 " --> pdb=" O LYS A 433 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 431 through 437' Processing helix chain 'A' and resid 456 through 467 removed outlier: 4.167A pdb=" N VAL A 460 " --> pdb=" O THR A 456 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N CYS A 467 " --> pdb=" O TRP A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 479 removed outlier: 3.517A pdb=" N GLU A 476 " --> pdb=" O TRP A 472 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASN A 477 " --> pdb=" O ASP A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 227 Processing helix chain 'B' and resid 230 through 238 removed outlier: 3.831A pdb=" N TRP B 234 " --> pdb=" O THR B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 246 Processing helix chain 'B' and resid 248 through 268 removed outlier: 3.575A pdb=" N GLN B 256 " --> pdb=" O SER B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 278 removed outlier: 3.972A pdb=" N PHE B 275 " --> pdb=" O PRO B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 289 Processing helix chain 'B' and resid 290 through 299 Processing helix chain 'B' and resid 302 through 314 Processing helix chain 'B' and resid 334 through 343 Processing helix chain 'B' and resid 380 through 390 removed outlier: 4.110A pdb=" N GLY B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 437 Processing helix chain 'B' and resid 457 through 470 removed outlier: 3.903A pdb=" N GLN B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN B 462 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN B 470 " --> pdb=" O TRP B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 480 Processing helix chain 'C' and resid 210 through 226 Processing helix chain 'C' and resid 230 through 238 Processing helix chain 'C' and resid 238 through 246 removed outlier: 3.594A pdb=" N TYR C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 268 Processing helix chain 'C' and resid 272 through 277 removed outlier: 3.619A pdb=" N LEU C 276 " --> pdb=" O THR C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 299 Processing helix chain 'C' and resid 302 through 315 removed outlier: 3.799A pdb=" N ASP C 315 " --> pdb=" O LEU C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 341 Processing helix chain 'C' and resid 380 through 390 removed outlier: 3.993A pdb=" N GLY C 390 " --> pdb=" O ALA C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 438 removed outlier: 3.893A pdb=" N ARG C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 470 removed outlier: 3.747A pdb=" N VAL C 460 " --> pdb=" O THR C 456 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN C 470 " --> pdb=" O TRP C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 480 removed outlier: 3.557A pdb=" N GLU C 476 " --> pdb=" O TRP C 472 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN C 477 " --> pdb=" O ASP C 473 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TRP C 478 " --> pdb=" O HIS C 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 226 Processing helix chain 'D' and resid 230 through 238 Processing helix chain 'D' and resid 238 through 246 removed outlier: 3.650A pdb=" N TYR D 242 " --> pdb=" O ASP D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 268 Processing helix chain 'D' and resid 272 through 277 removed outlier: 3.763A pdb=" N LEU D 276 " --> pdb=" O THR D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 299 Processing helix chain 'D' and resid 302 through 314 Processing helix chain 'D' and resid 333 through 343 Processing helix chain 'D' and resid 380 through 390 removed outlier: 4.180A pdb=" N GLY D 390 " --> pdb=" O ALA D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 437 removed outlier: 4.281A pdb=" N LYS D 436 " --> pdb=" O LYS D 433 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLU D 437 " --> pdb=" O ALA D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 453 removed outlier: 4.221A pdb=" N GLY D 453 " --> pdb=" O PRO D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 469 removed outlier: 3.573A pdb=" N VAL D 460 " --> pdb=" O THR D 456 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA D 469 " --> pdb=" O THR D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 480 Processing helix chain 'D' and resid 495 through 499 Processing helix chain 'E' and resid 210 through 226 Processing helix chain 'E' and resid 230 through 238 Processing helix chain 'E' and resid 238 through 246 removed outlier: 3.599A pdb=" N TYR E 242 " --> pdb=" O ASP E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 268 Processing helix chain 'E' and resid 271 through 276 removed outlier: 4.211A pdb=" N PHE E 275 " --> pdb=" O PRO E 271 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU E 276 " --> pdb=" O THR E 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 271 through 276' Processing helix chain 'E' and resid 290 through 299 Processing helix chain 'E' and resid 302 through 315 removed outlier: 3.802A pdb=" N GLY E 307 " --> pdb=" O PRO E 303 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP E 315 " --> pdb=" O LEU E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 343 Processing helix chain 'E' and resid 380 through 388 Processing helix chain 'E' and resid 431 through 438 removed outlier: 3.798A pdb=" N ARG E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 469 removed outlier: 3.835A pdb=" N VAL E 460 " --> pdb=" O THR E 456 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA E 469 " --> pdb=" O THR E 465 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 478 Processing helix chain 'E' and resid 490 through 494 removed outlier: 3.901A pdb=" N LEU E 494 " --> pdb=" O ALA E 491 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 499 Processing helix chain 'F' and resid 210 through 226 removed outlier: 3.633A pdb=" N ILE F 214 " --> pdb=" O THR F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 238 Processing helix chain 'F' and resid 238 through 246 removed outlier: 3.689A pdb=" N TYR F 242 " --> pdb=" O ASP F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 268 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 290 through 299 Processing helix chain 'F' and resid 302 through 314 removed outlier: 3.663A pdb=" N VAL F 306 " --> pdb=" O ASP F 302 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU F 311 " --> pdb=" O GLY F 307 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS F 312 " --> pdb=" O GLN F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 343 removed outlier: 3.892A pdb=" N LEU F 337 " --> pdb=" O GLY F 333 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA F 338 " --> pdb=" O LYS F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 388 removed outlier: 3.529A pdb=" N ALA F 384 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS F 385 " --> pdb=" O VAL F 381 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA F 386 " --> pdb=" O GLU F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 437 removed outlier: 3.838A pdb=" N LYS F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA F 434 " --> pdb=" O VAL F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 469 removed outlier: 4.070A pdb=" N VAL F 460 " --> pdb=" O THR F 456 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA F 469 " --> pdb=" O THR F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 479 Processing sheet with id=AA1, first strand: chain 'A' and resid 349 through 350 removed outlier: 6.943A pdb=" N GLY A 349 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N ASP A 372 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL A 369 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N THR A 413 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N TRP A 371 " --> pdb=" O THR A 413 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU A 324 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N SER A 414 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE A 326 " --> pdb=" O SER A 414 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 348 through 350 removed outlier: 6.315A pdb=" N VAL B 369 " --> pdb=" O VAL B 411 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N THR B 413 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP B 371 " --> pdb=" O THR B 413 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU B 324 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N SER B 414 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N PHE B 326 " --> pdb=" O SER B 414 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 393 through 396 Processing sheet with id=AA4, first strand: chain 'B' and resid 421 through 423 Processing sheet with id=AA5, first strand: chain 'C' and resid 349 through 350 removed outlier: 6.550A pdb=" N GLY C 349 " --> pdb=" O VAL C 370 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ASP C 372 " --> pdb=" O GLY C 349 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 393 through 395 Processing sheet with id=AA7, first strand: chain 'C' and resid 421 through 423 Processing sheet with id=AA8, first strand: chain 'D' and resid 349 through 350 removed outlier: 7.020A pdb=" N GLY D 349 " --> pdb=" O VAL D 370 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ASP D 372 " --> pdb=" O GLY D 349 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU D 324 " --> pdb=" O ILE D 412 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N SER D 414 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE D 326 " --> pdb=" O SER D 414 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 421 through 423 Processing sheet with id=AB1, first strand: chain 'E' and resid 325 through 327 Processing sheet with id=AB2, first strand: chain 'E' and resid 422 through 423 removed outlier: 3.507A pdb=" N THR E 426 " --> pdb=" O SER E 423 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 348 through 350 removed outlier: 5.827A pdb=" N GLY F 349 " --> pdb=" O VAL F 370 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL F 369 " --> pdb=" O VAL F 411 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N THR F 413 " --> pdb=" O VAL F 369 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TRP F 371 " --> pdb=" O THR F 413 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N TRP F 325 " --> pdb=" O LEU F 442 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 422 through 423 removed outlier: 3.530A pdb=" N THR F 426 " --> pdb=" O SER F 423 " (cutoff:3.500A) 525 hydrogen bonds defined for protein. 1503 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.09 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2209 1.32 - 1.44: 3867 1.44 - 1.57: 7886 1.57 - 1.69: 43 1.69 - 1.82: 110 Bond restraints: 14115 Sorted by residual: bond pdb=" N3B ANP D 601 " pdb=" PG ANP D 601 " ideal model delta sigma weight residual 1.795 1.617 0.178 2.00e-02 2.50e+03 7.93e+01 bond pdb=" O3A ANP C 601 " pdb=" PB ANP C 601 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.30e+01 bond pdb=" O3A ANP B 601 " pdb=" PB ANP B 601 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.26e+01 bond pdb=" O3A ANP A 601 " pdb=" PB ANP A 601 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.22e+01 bond pdb=" O3A ANP E 601 " pdb=" PB ANP E 601 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.22e+01 ... (remaining 14110 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.79: 19169 3.79 - 7.57: 99 7.57 - 11.36: 18 11.36 - 15.14: 0 15.14 - 18.93: 4 Bond angle restraints: 19290 Sorted by residual: angle pdb=" PB ANP E 601 " pdb=" N3B ANP E 601 " pdb=" PG ANP E 601 " ideal model delta sigma weight residual 126.95 108.02 18.93 3.00e+00 1.11e-01 3.98e+01 angle pdb=" PB ANP C 601 " pdb=" N3B ANP C 601 " pdb=" PG ANP C 601 " ideal model delta sigma weight residual 126.95 108.82 18.13 3.00e+00 1.11e-01 3.65e+01 angle pdb=" PB ANP B 601 " pdb=" N3B ANP B 601 " pdb=" PG ANP B 601 " ideal model delta sigma weight residual 126.95 109.28 17.67 3.00e+00 1.11e-01 3.47e+01 angle pdb=" PB ANP F 601 " pdb=" N3B ANP F 601 " pdb=" PG ANP F 601 " ideal model delta sigma weight residual 126.95 109.83 17.12 3.00e+00 1.11e-01 3.26e+01 angle pdb=" N SER E 367 " pdb=" CA SER E 367 " pdb=" C SER E 367 " ideal model delta sigma weight residual 114.62 108.93 5.69 1.14e+00 7.69e-01 2.49e+01 ... (remaining 19285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.42: 8025 31.42 - 62.83: 263 62.83 - 94.25: 54 94.25 - 125.66: 0 125.66 - 157.08: 1 Dihedral angle restraints: 8343 sinusoidal: 3316 harmonic: 5027 Sorted by residual: dihedral pdb=" C4' DT H 4 " pdb=" C3' DT H 4 " pdb=" O3' DT H 4 " pdb=" P DT H 5 " ideal model delta sinusoidal sigma weight residual 220.00 62.92 157.08 1 3.50e+01 8.16e-04 1.51e+01 dihedral pdb=" CA ASP B 473 " pdb=" C ASP B 473 " pdb=" N HIS B 474 " pdb=" CA HIS B 474 " ideal model delta harmonic sigma weight residual 180.00 162.71 17.29 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ASP A 232 " pdb=" CB ASP A 232 " pdb=" CG ASP A 232 " pdb=" OD1 ASP A 232 " ideal model delta sinusoidal sigma weight residual -30.00 -88.19 58.19 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 8340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1955 0.067 - 0.133: 236 0.133 - 0.200: 6 0.200 - 0.267: 2 0.267 - 0.334: 6 Chirality restraints: 2205 Sorted by residual: chirality pdb=" C3' ANP D 601 " pdb=" C2' ANP D 601 " pdb=" C4' ANP D 601 " pdb=" O3' ANP D 601 " both_signs ideal model delta sigma weight residual False -2.36 -2.69 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" C3' ANP A 601 " pdb=" C2' ANP A 601 " pdb=" C4' ANP A 601 " pdb=" O3' ANP A 601 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C3' ANP F 601 " pdb=" C2' ANP F 601 " pdb=" C4' ANP F 601 " pdb=" O3' ANP F 601 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 2202 not shown) Planarity restraints: 2357 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 270 " -0.057 5.00e-02 4.00e+02 8.49e-02 1.15e+01 pdb=" N PRO F 271 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO F 271 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO F 271 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 496 " 0.011 2.00e-02 2.50e+03 2.11e-02 4.47e+00 pdb=" C PRO A 496 " -0.037 2.00e-02 2.50e+03 pdb=" O PRO A 496 " 0.014 2.00e-02 2.50e+03 pdb=" N ASP A 497 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 495 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO A 496 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 496 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 496 " 0.024 5.00e-02 4.00e+02 ... (remaining 2354 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 207 2.66 - 3.22: 13027 3.22 - 3.78: 20466 3.78 - 4.34: 27140 4.34 - 4.90: 45517 Nonbonded interactions: 106357 Sorted by model distance: nonbonded pdb=" O3G ANP D 601 " pdb="MG MG D 602 " model vdw 2.103 2.170 nonbonded pdb=" OG1 THR B 335 " pdb="MG MG B 602 " model vdw 2.104 2.170 nonbonded pdb=" O1G ANP C 601 " pdb="MG MG C 602 " model vdw 2.105 2.170 nonbonded pdb=" OE2 GLU A 231 " pdb=" OH TYR A 242 " model vdw 2.158 3.040 nonbonded pdb=" O1B ANP C 601 " pdb=" O3G ANP C 601 " model vdw 2.160 3.040 ... (remaining 106352 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 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 202 and (name N or name CA or name C or name O or name CB \ )) or resid 203 through 277 or resid 286 through 319 or (resid 320 and (name N \ or name CA or name C or name O or name CB )) or resid 321 through 349 or (resid \ 350 and (name N or name CA or name C or name O or name CB )) or resid 351 throug \ h 352 or (resid 353 and (name N or name CA or name C or name O or name CB )) or \ resid 354 through 355 or (resid 356 through 358 and (name N or name CA or name C \ or name O or name CB )) or resid 359 through 360 or (resid 361 through 362 and \ (name N or name CA or name C or name O or name CB )) or resid 363 through 372 or \ (resid 373 and (name N or name CA or name C or name O or name CB )) or resid 37 \ 4 or (resid 375 and (name N or name CA or name C or name O or name CB )) or resi \ d 376 through 421 or (resid 422 and (name N or name CA or name C or name O or na \ me CB )) or resid 423 through 432 or (resid 433 through 434 and (name N or name \ CA or name C or name O or name CB )) or resid 435 or (resid 436 through 438 and \ (name N or name CA or name C or name O or name CB )) or resid 439 through 446 or \ (resid 447 and (name N or name CA or name C or name O or name CB )) or resid 44 \ 8 through 476 or (resid 477 and (name N or name CA or name C or name O or name C \ B )) or resid 478 through 486)) selection = (chain 'B' and ((resid 202 and (name N or name CA or name C or name O or name CB \ )) or resid 203 through 226 or (resid 227 and (name N or name CA or name C or n \ ame O or name CB )) or resid 228 through 277 or resid 286 through 287 or (resid \ 288 through 290 and (name N or name CA or name C or name O or name CB )) or resi \ d 291 through 299 or (resid 300 and (name N or name CA or name C or name O or na \ me CB )) or resid 301 through 307 or (resid 308 and (name N or name CA or name C \ or name O or name CB )) or resid 309 through 319 or (resid 320 and (name N or n \ ame CA or name C or name O or name CB )) or resid 321 or (resid 322 and (name N \ or name CA or name C or name O or name CB )) or resid 323 through 328 or (resid \ 329 and (name N or name CA or name C or name O or name CB )) or resid 330 throug \ h 349 or (resid 350 and (name N or name CA or name C or name O or name CB )) or \ resid 351 through 352 or (resid 353 and (name N or name CA or name C or name O o \ r name CB )) or resid 354 through 355 or (resid 356 through 358 and (name N or n \ ame CA or name C or name O or name CB )) or resid 359 through 360 or (resid 361 \ through 362 and (name N or name CA or name C or name O or name CB )) or resid 36 \ 3 through 374 or (resid 375 and (name N or name CA or name C or name O or name C \ B )) or resid 376 through 380 or (resid 381 through 384 and (name N or name CA o \ r name C or name O or name CB )) or resid 385 through 421 or (resid 422 and (nam \ e N or name CA or name C or name O or name CB )) or resid 423 through 432 or (re \ sid 433 through 434 and (name N or name CA or name C or name O or name CB )) or \ resid 435 or (resid 436 through 438 and (name N or name CA or name C or name O o \ r name CB )) or resid 439 through 446 or (resid 447 and (name N or name CA or na \ me C or name O or name CB )) or resid 448 through 453 or (resid 454 and (name N \ or name CA or name C or name O or name CB )) or resid 455 through 469 or (resid \ 470 and (name N or name CA or name C or name O or name CB )) or resid 471 throug \ h 476 or (resid 477 and (name N or name CA or name C or name O or name CB )) or \ resid 478 through 486)) selection = (chain 'C' and ((resid 202 and (name N or name CA or name C or name O or name CB \ )) or resid 203 through 226 or (resid 227 and (name N or name CA or name C or n \ ame O or name CB )) or resid 228 through 277 or resid 286 through 287 or (resid \ 288 through 290 and (name N or name CA or name C or name O or name CB )) or resi \ d 291 through 299 or (resid 300 and (name N or name CA or name C or name O or na \ me CB )) or resid 301 through 307 or (resid 308 and (name N or name CA or name C \ or name O or name CB )) or resid 309 through 319 or (resid 320 and (name N or n \ ame CA or name C or name O or name CB )) or resid 321 or (resid 322 and (name N \ or name CA or name C or name O or name CB )) or resid 323 through 328 or (resid \ 329 and (name N or name CA or name C or name O or name CB )) or resid 330 throug \ h 349 or (resid 350 and (name N or name CA or name C or name O or name CB )) or \ resid 351 through 352 or (resid 353 and (name N or name CA or name C or name O o \ r name CB )) or resid 354 through 355 or (resid 356 through 358 and (name N or n \ ame CA or name C or name O or name CB )) or resid 359 through 360 or (resid 361 \ through 362 and (name N or name CA or name C or name O or name CB )) or resid 36 \ 3 through 372 or (resid 373 and (name N or name CA or name C or name O or name C \ B )) or resid 374 or (resid 375 and (name N or name CA or name C or name O or na \ me CB )) or resid 376 through 380 or (resid 381 through 384 and (name N or name \ CA or name C or name O or name CB )) or resid 385 through 421 or (resid 422 and \ (name N or name CA or name C or name O or name CB )) or resid 423 through 432 or \ (resid 433 through 434 and (name N or name CA or name C or name O or name CB )) \ or resid 435 or (resid 436 through 438 and (name N or name CA or name C or name \ O or name CB )) or resid 439 through 446 or (resid 447 and (name N or name CA o \ r name C or name O or name CB )) or resid 448 through 453 or (resid 454 and (nam \ e N or name CA or name C or name O or name CB )) or resid 455 through 469 or (re \ sid 470 and (name N or name CA or name C or name O or name CB )) or resid 471 th \ rough 476 or (resid 477 and (name N or name CA or name C or name O or name CB )) \ or resid 478 through 486)) selection = (chain 'D' and ((resid 202 and (name N or name CA or name C or name O or name CB \ )) or resid 203 through 226 or (resid 227 and (name N or name CA or name C or n \ ame O or name CB )) or resid 228 through 277 or resid 286 through 287 or (resid \ 288 through 290 and (name N or name CA or name C or name O or name CB )) or resi \ d 291 through 299 or (resid 300 and (name N or name CA or name C or name O or na \ me CB )) or resid 301 through 307 or (resid 308 and (name N or name CA or name C \ or name O or name CB )) or resid 309 through 319 or (resid 320 and (name N or n \ ame CA or name C or name O or name CB )) or resid 321 or (resid 322 and (name N \ or name CA or name C or name O or name CB )) or resid 323 through 328 or (resid \ 329 and (name N or name CA or name C or name O or name CB )) or resid 330 throug \ h 349 or (resid 350 and (name N or name CA or name C or name O or name CB )) or \ resid 351 through 352 or (resid 353 and (name N or name CA or name C or name O o \ r name CB )) or resid 354 through 355 or (resid 356 through 358 and (name N or n \ ame CA or name C or name O or name CB )) or resid 359 through 360 or (resid 361 \ through 362 and (name N or name CA or name C or name O or name CB )) or resid 36 \ 3 through 372 or (resid 373 and (name N or name CA or name C or name O or name C \ B )) or resid 374 or (resid 375 and (name N or name CA or name C or name O or na \ me CB )) or resid 376 through 380 or (resid 381 through 384 and (name N or name \ CA or name C or name O or name CB )) or resid 385 through 421 or (resid 422 and \ (name N or name CA or name C or name O or name CB )) or resid 423 through 432 or \ (resid 433 through 434 and (name N or name CA or name C or name O or name CB )) \ or resid 435 or (resid 436 through 438 and (name N or name CA or name C or name \ O or name CB )) or resid 439 through 446 or (resid 447 and (name N or name CA o \ r name C or name O or name CB )) or resid 448 through 453 or (resid 454 and (nam \ e N or name CA or name C or name O or name CB )) or resid 455 through 469 or (re \ sid 470 and (name N or name CA or name C or name O or name CB )) or resid 471 th \ rough 476 or (resid 477 and (name N or name CA or name C or name O or name CB )) \ or resid 478 through 486)) selection = (chain 'E' and ((resid 202 and (name N or name CA or name C or name O or name CB \ )) or resid 203 through 226 or (resid 227 and (name N or name CA or name C or n \ ame O or name CB )) or resid 228 through 277 or resid 286 through 287 or (resid \ 288 through 290 and (name N or name CA or name C or name O or name CB )) or resi \ d 291 through 299 or (resid 300 and (name N or name CA or name C or name O or na \ me CB )) or resid 301 through 307 or (resid 308 and (name N or name CA or name C \ or name O or name CB )) or resid 309 through 319 or (resid 320 and (name N or n \ ame CA or name C or name O or name CB )) or resid 321 or (resid 322 and (name N \ or name CA or name C or name O or name CB )) or resid 323 through 328 or (resid \ 329 and (name N or name CA or name C or name O or name CB )) or resid 330 throug \ h 349 or (resid 350 and (name N or name CA or name C or name O or name CB )) or \ resid 351 through 352 or (resid 353 and (name N or name CA or name C or name O o \ r name CB )) or resid 354 through 355 or (resid 356 through 358 and (name N or n \ ame CA or name C or name O or name CB )) or resid 359 through 360 or (resid 361 \ through 362 and (name N or name CA or name C or name O or name CB )) or resid 36 \ 3 through 372 or (resid 373 and (name N or name CA or name C or name O or name C \ B )) or resid 374 or (resid 375 and (name N or name CA or name C or name O or na \ me CB )) or resid 376 through 380 or (resid 381 through 384 and (name N or name \ CA or name C or name O or name CB )) or resid 385 through 421 or (resid 422 and \ (name N or name CA or name C or name O or name CB )) or resid 423 through 432 or \ (resid 433 through 434 and (name N or name CA or name C or name O or name CB )) \ or resid 435 or (resid 436 through 438 and (name N or name CA or name C or name \ O or name CB )) or resid 439 through 446 or (resid 447 and (name N or name CA o \ r name C or name O or name CB )) or resid 448 through 453 or (resid 454 and (nam \ e N or name CA or name C or name O or name CB )) or resid 455 through 469 or (re \ sid 470 and (name N or name CA or name C or name O or name CB )) or resid 471 th \ rough 476 or (resid 477 and (name N or name CA or name C or name O or name CB )) \ or resid 478 through 486)) selection = (chain 'F' and (resid 202 through 226 or (resid 227 and (name N or name CA or na \ me C or name O or name CB )) or resid 228 through 287 or (resid 288 through 290 \ and (name N or name CA or name C or name O or name CB )) or resid 291 through 29 \ 9 or (resid 300 and (name N or name CA or name C or name O or name CB )) or resi \ d 301 through 307 or (resid 308 and (name N or name CA or name C or name O or na \ me CB )) or resid 309 through 321 or (resid 322 and (name N or name CA or name C \ or name O or name CB )) or resid 323 through 380 or (resid 381 through 384 and \ (name N or name CA or name C or name O or name CB )) or resid 385 through 399 or \ (resid 400 and (name N or name CA or name C or name O or name CB )) or resid 40 \ 1 through 437 or (resid 438 and (name N or name CA or name C or name O or name C \ B )) or resid 439 through 453 or (resid 454 and (name N or name CA or name C or \ name O or name CB )) or resid 455 through 469 or (resid 470 and (name N or name \ CA or name C or name O or name CB )) or resid 471 through 486)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 13.840 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 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 : 0.006 0.178 14115 Z= 0.288 Angle : 0.757 18.926 19290 Z= 0.368 Chirality : 0.045 0.334 2205 Planarity : 0.004 0.085 2357 Dihedral : 16.262 157.078 5083 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.71 % Favored : 92.76 % Rotamer: Outliers : 0.76 % Allowed : 0.82 % Favored : 98.42 % 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: 0.26 (0.21), residues: 1713 helix: 1.50 (0.20), residues: 753 sheet: 0.76 (0.42), residues: 188 loop : -1.38 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 438 TYR 0.012 0.001 TYR E 264 PHE 0.009 0.001 PHE C 444 TRP 0.012 0.001 TRP A 463 HIS 0.004 0.001 HIS B 495 Details of bonding type rmsd covalent geometry : bond 0.00569 (14115) covalent geometry : angle 0.75705 (19290) hydrogen bonds : bond 0.14627 ( 525) hydrogen bonds : angle 4.98230 ( 1503) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 0.539 Fit side-chains REVERT: A 361 ASN cc_start: 0.8495 (OUTLIER) cc_final: 0.8133 (m-40) REVERT: B 399 MET cc_start: 0.8322 (mmt) cc_final: 0.7960 (mmp) REVERT: C 438 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8253 (mtt180) REVERT: E 357 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.8111 (t0) REVERT: F 324 LEU cc_start: 0.6258 (mm) cc_final: 0.6053 (mm) outliers start: 11 outliers final: 2 residues processed: 169 average time/residue: 0.1157 time to fit residues: 29.3158 Evaluate side-chains 138 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 133 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain C residue 438 ARG Chi-restraints excluded: chain E residue 357 ASN Chi-restraints excluded: chain E residue 375 ILE Chi-restraints excluded: chain E residue 396 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN B 268 ASN B 309 HIS C 226 ASN C 361 ASN E 357 ASN E 397 GLN F 300 ASN F 397 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.109147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.082365 restraints weight = 31398.750| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.92 r_work: 0.3030 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14115 Z= 0.110 Angle : 0.527 11.051 19290 Z= 0.273 Chirality : 0.041 0.156 2205 Planarity : 0.004 0.055 2357 Dihedral : 11.658 156.790 2056 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.36 % Favored : 93.29 % Rotamer: Outliers : 0.62 % Allowed : 7.49 % Favored : 91.90 % 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: 0.46 (0.21), residues: 1713 helix: 1.70 (0.20), residues: 744 sheet: 0.82 (0.41), residues: 187 loop : -1.26 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 227 TYR 0.011 0.001 TYR A 348 PHE 0.027 0.001 PHE E 205 TRP 0.011 0.001 TRP B 466 HIS 0.003 0.001 HIS A 495 Details of bonding type rmsd covalent geometry : bond 0.00241 (14115) covalent geometry : angle 0.52733 (19290) hydrogen bonds : bond 0.03854 ( 525) hydrogen bonds : angle 3.82579 ( 1503) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 0.583 Fit side-chains REVERT: A 362 ASP cc_start: 0.8904 (p0) cc_final: 0.8668 (p0) REVERT: B 208 LYS cc_start: 0.7175 (mmmt) cc_final: 0.6925 (mmmt) REVERT: C 225 GLU cc_start: 0.9044 (tm-30) cc_final: 0.8782 (tm-30) REVERT: E 244 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8767 (tp) REVERT: E 357 ASN cc_start: 0.8736 (t0) cc_final: 0.8076 (t0) REVERT: F 294 LYS cc_start: 0.7182 (tmmt) cc_final: 0.6748 (pttp) REVERT: F 399 MET cc_start: 0.6033 (mmt) cc_final: 0.5579 (pmm) outliers start: 9 outliers final: 4 residues processed: 151 average time/residue: 0.1172 time to fit residues: 26.6323 Evaluate side-chains 137 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain C residue 361 ASN Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 244 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 53 optimal weight: 7.9990 chunk 73 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 0.0370 overall best weight: 0.9464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN A 361 ASN ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 GLN C 361 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.108846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.082081 restraints weight = 31385.707| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.92 r_work: 0.3025 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14115 Z= 0.103 Angle : 0.484 5.932 19290 Z= 0.253 Chirality : 0.041 0.148 2205 Planarity : 0.004 0.054 2357 Dihedral : 10.122 156.857 2044 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.25 % Favored : 93.58 % Rotamer: Outliers : 0.69 % Allowed : 9.41 % Favored : 89.90 % 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: 0.52 (0.21), residues: 1713 helix: 1.74 (0.20), residues: 745 sheet: 0.86 (0.41), residues: 188 loop : -1.22 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 438 TYR 0.007 0.001 TYR F 482 PHE 0.009 0.001 PHE C 360 TRP 0.016 0.001 TRP F 463 HIS 0.011 0.001 HIS F 431 Details of bonding type rmsd covalent geometry : bond 0.00232 (14115) covalent geometry : angle 0.48352 (19290) hydrogen bonds : bond 0.03534 ( 525) hydrogen bonds : angle 3.61679 ( 1503) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.555 Fit side-chains REVERT: A 362 ASP cc_start: 0.8868 (p0) cc_final: 0.8555 (p0) REVERT: A 398 LYS cc_start: 0.7106 (mttt) cc_final: 0.6410 (mtpt) REVERT: A 472 TRP cc_start: 0.7963 (m-10) cc_final: 0.7055 (m-10) REVERT: B 208 LYS cc_start: 0.7153 (mmmt) cc_final: 0.6753 (mmmt) REVERT: E 244 LEU cc_start: 0.9096 (tp) cc_final: 0.8800 (tp) REVERT: E 357 ASN cc_start: 0.8720 (t0) cc_final: 0.8068 (t0) REVERT: E 399 MET cc_start: 0.6244 (mmm) cc_final: 0.6003 (mmm) REVERT: F 399 MET cc_start: 0.5808 (mmt) cc_final: 0.5502 (pmm) outliers start: 10 outliers final: 8 residues processed: 147 average time/residue: 0.1115 time to fit residues: 25.0168 Evaluate side-chains 139 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 361 ASN Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 457 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 457 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 72 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 157 optimal weight: 0.0370 chunk 170 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 overall best weight: 1.5064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 GLN ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 ASN E 309 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.107743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.081144 restraints weight = 31505.427| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.91 r_work: 0.3009 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14115 Z= 0.128 Angle : 0.493 7.660 19290 Z= 0.260 Chirality : 0.041 0.188 2205 Planarity : 0.004 0.052 2357 Dihedral : 9.777 156.954 2044 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.42 % Favored : 93.40 % Rotamer: Outliers : 1.03 % Allowed : 11.06 % Favored : 87.91 % 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: 0.49 (0.21), residues: 1713 helix: 1.67 (0.20), residues: 752 sheet: 0.76 (0.40), residues: 195 loop : -1.22 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 438 TYR 0.010 0.001 TYR E 475 PHE 0.012 0.001 PHE B 358 TRP 0.017 0.001 TRP F 463 HIS 0.011 0.001 HIS F 431 Details of bonding type rmsd covalent geometry : bond 0.00300 (14115) covalent geometry : angle 0.49285 (19290) hydrogen bonds : bond 0.03739 ( 525) hydrogen bonds : angle 3.63428 ( 1503) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.639 Fit side-chains REVERT: A 397 GLN cc_start: 0.7855 (mt0) cc_final: 0.7617 (mm-40) REVERT: A 398 LYS cc_start: 0.7086 (mttt) cc_final: 0.6400 (mtpt) REVERT: A 472 TRP cc_start: 0.7953 (m-10) cc_final: 0.7023 (m-10) REVERT: B 208 LYS cc_start: 0.7122 (mmmt) cc_final: 0.6694 (mmmt) REVERT: E 244 LEU cc_start: 0.9120 (tp) cc_final: 0.8833 (tp) REVERT: E 357 ASN cc_start: 0.8696 (t0) cc_final: 0.8080 (t0) REVERT: E 399 MET cc_start: 0.6562 (mmm) cc_final: 0.6324 (mmm) REVERT: F 294 LYS cc_start: 0.7330 (ptmt) cc_final: 0.7041 (pttp) REVERT: F 399 MET cc_start: 0.5813 (mmt) cc_final: 0.5521 (pmm) outliers start: 15 outliers final: 10 residues processed: 148 average time/residue: 0.1207 time to fit residues: 27.2674 Evaluate side-chains 138 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 361 ASN Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 457 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain F residue 421 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 135 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 137 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.108843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.082154 restraints weight = 31494.954| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.93 r_work: 0.3029 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14115 Z= 0.097 Angle : 0.478 7.680 19290 Z= 0.252 Chirality : 0.041 0.176 2205 Planarity : 0.004 0.052 2357 Dihedral : 9.579 157.123 2044 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.30 % Favored : 93.52 % Rotamer: Outliers : 1.24 % Allowed : 11.95 % Favored : 86.81 % 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 (0.21), residues: 1713 helix: 1.70 (0.20), residues: 753 sheet: 0.81 (0.40), residues: 196 loop : -1.16 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 438 TYR 0.008 0.001 TYR C 242 PHE 0.021 0.001 PHE E 205 TRP 0.018 0.001 TRP F 463 HIS 0.011 0.001 HIS F 431 Details of bonding type rmsd covalent geometry : bond 0.00217 (14115) covalent geometry : angle 0.47824 (19290) hydrogen bonds : bond 0.03278 ( 525) hydrogen bonds : angle 3.52508 ( 1503) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: A 397 GLN cc_start: 0.7869 (mt0) cc_final: 0.7603 (mm-40) REVERT: A 398 LYS cc_start: 0.7003 (mttt) cc_final: 0.6385 (mtpt) REVERT: A 472 TRP cc_start: 0.7978 (m-10) cc_final: 0.7123 (m-10) REVERT: B 208 LYS cc_start: 0.7181 (mmmt) cc_final: 0.6788 (mmmt) REVERT: E 244 LEU cc_start: 0.9110 (tp) cc_final: 0.8823 (tp) REVERT: E 357 ASN cc_start: 0.8665 (t0) cc_final: 0.8047 (t0) REVERT: E 399 MET cc_start: 0.6544 (mmm) cc_final: 0.6300 (mmm) outliers start: 18 outliers final: 12 residues processed: 155 average time/residue: 0.1120 time to fit residues: 26.5908 Evaluate side-chains 144 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 457 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 457 GLU Chi-restraints excluded: chain F residue 421 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 85 optimal weight: 3.9990 chunk 80 optimal weight: 0.1980 chunk 112 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 169 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 309 HIS ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 300 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 = 0.3531 r_free = 0.3531 target = 0.105185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.078580 restraints weight = 31447.021| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.00 r_work: 0.2958 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14115 Z= 0.211 Angle : 0.569 7.810 19290 Z= 0.300 Chirality : 0.043 0.154 2205 Planarity : 0.004 0.047 2357 Dihedral : 9.861 158.082 2044 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.41 % Favored : 92.35 % Rotamer: Outliers : 1.72 % Allowed : 12.02 % Favored : 86.26 % 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: 0.33 (0.21), residues: 1713 helix: 1.57 (0.20), residues: 744 sheet: 0.70 (0.40), residues: 181 loop : -1.28 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 438 TYR 0.012 0.001 TYR A 264 PHE 0.015 0.001 PHE D 205 TRP 0.017 0.001 TRP F 463 HIS 0.008 0.001 HIS F 431 Details of bonding type rmsd covalent geometry : bond 0.00492 (14115) covalent geometry : angle 0.56877 (19290) hydrogen bonds : bond 0.04965 ( 525) hydrogen bonds : angle 3.90355 ( 1503) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 398 LYS cc_start: 0.6979 (mttt) cc_final: 0.6388 (mtpt) REVERT: B 208 LYS cc_start: 0.7424 (mmmt) cc_final: 0.6948 (mmmt) REVERT: B 238 ASP cc_start: 0.8359 (t0) cc_final: 0.8112 (t0) REVERT: E 244 LEU cc_start: 0.9144 (tp) cc_final: 0.8855 (tp) REVERT: E 357 ASN cc_start: 0.8512 (t0) cc_final: 0.7864 (t0) outliers start: 25 outliers final: 19 residues processed: 159 average time/residue: 0.1053 time to fit residues: 25.5656 Evaluate side-chains 152 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 457 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 457 GLU Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 421 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 91 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 102 optimal weight: 0.4980 chunk 2 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 137 optimal weight: 0.0980 chunk 146 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN B 309 HIS ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 300 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 = 0.3576 r_free = 0.3576 target = 0.107893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.081521 restraints weight = 31466.894| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.91 r_work: 0.3013 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14115 Z= 0.101 Angle : 0.500 8.444 19290 Z= 0.266 Chirality : 0.041 0.201 2205 Planarity : 0.004 0.053 2357 Dihedral : 9.544 156.734 2044 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.84 % Favored : 93.93 % Rotamer: Outliers : 1.37 % Allowed : 12.84 % Favored : 85.78 % 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 (0.21), residues: 1713 helix: 1.67 (0.20), residues: 749 sheet: 0.78 (0.40), residues: 186 loop : -1.09 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 438 TYR 0.008 0.001 TYR C 242 PHE 0.028 0.001 PHE E 205 TRP 0.043 0.001 TRP F 463 HIS 0.007 0.001 HIS F 431 Details of bonding type rmsd covalent geometry : bond 0.00223 (14115) covalent geometry : angle 0.49986 (19290) hydrogen bonds : bond 0.03343 ( 525) hydrogen bonds : angle 3.55840 ( 1503) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 352 ASN cc_start: 0.7133 (m110) cc_final: 0.6708 (t0) REVERT: A 397 GLN cc_start: 0.8110 (mt0) cc_final: 0.7549 (mm-40) REVERT: A 398 LYS cc_start: 0.6933 (mttt) cc_final: 0.6287 (mtpt) REVERT: A 472 TRP cc_start: 0.7976 (m-10) cc_final: 0.7163 (m-10) REVERT: B 208 LYS cc_start: 0.7476 (mmmt) cc_final: 0.7039 (mmmt) REVERT: C 225 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8670 (tm-30) REVERT: E 244 LEU cc_start: 0.9128 (tp) cc_final: 0.8855 (tp) REVERT: E 357 ASN cc_start: 0.8588 (t0) cc_final: 0.7929 (t0) outliers start: 20 outliers final: 14 residues processed: 167 average time/residue: 0.1045 time to fit residues: 26.9734 Evaluate side-chains 153 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 457 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 457 GLU Chi-restraints excluded: chain F residue 413 THR Chi-restraints excluded: chain F residue 421 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 155 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 166 optimal weight: 0.0980 chunk 77 optimal weight: 0.0070 chunk 15 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 23 optimal weight: 0.6980 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.108767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.082181 restraints weight = 31101.113| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 3.04 r_work: 0.3021 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 14115 Z= 0.106 Angle : 0.513 14.320 19290 Z= 0.269 Chirality : 0.041 0.322 2205 Planarity : 0.004 0.052 2357 Dihedral : 9.440 157.067 2044 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.30 % Favored : 93.46 % Rotamer: Outliers : 1.17 % Allowed : 13.53 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.21), residues: 1713 helix: 1.75 (0.20), residues: 749 sheet: 0.73 (0.39), residues: 195 loop : -1.10 (0.23), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 438 TYR 0.008 0.001 TYR C 242 PHE 0.007 0.001 PHE A 486 TRP 0.032 0.001 TRP F 463 HIS 0.005 0.001 HIS F 431 Details of bonding type rmsd covalent geometry : bond 0.00251 (14115) covalent geometry : angle 0.51288 (19290) hydrogen bonds : bond 0.03239 ( 525) hydrogen bonds : angle 3.50617 ( 1503) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 352 ASN cc_start: 0.7148 (m110) cc_final: 0.6751 (t0) REVERT: A 397 GLN cc_start: 0.8118 (mt0) cc_final: 0.7519 (mm-40) REVERT: A 398 LYS cc_start: 0.6831 (mttt) cc_final: 0.6166 (mtpt) REVERT: A 472 TRP cc_start: 0.8030 (m-10) cc_final: 0.7073 (m-10) REVERT: B 208 LYS cc_start: 0.7363 (mmmt) cc_final: 0.6878 (mmmt) REVERT: E 244 LEU cc_start: 0.9119 (tp) cc_final: 0.8845 (tp) REVERT: E 357 ASN cc_start: 0.8592 (t0) cc_final: 0.7899 (t0) outliers start: 17 outliers final: 16 residues processed: 155 average time/residue: 0.0968 time to fit residues: 23.1836 Evaluate side-chains 152 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 457 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 457 GLU Chi-restraints excluded: chain F residue 413 THR Chi-restraints excluded: chain F residue 421 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 168 optimal weight: 0.0670 chunk 122 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.108044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.081418 restraints weight = 31339.132| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.04 r_work: 0.3009 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 14115 Z= 0.119 Angle : 0.518 12.869 19290 Z= 0.271 Chirality : 0.041 0.252 2205 Planarity : 0.004 0.052 2357 Dihedral : 9.461 157.271 2044 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.36 % Favored : 93.40 % Rotamer: Outliers : 1.17 % Allowed : 13.46 % Favored : 85.37 % 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: 0.60 (0.21), residues: 1713 helix: 1.78 (0.20), residues: 750 sheet: 0.77 (0.39), residues: 191 loop : -1.13 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 438 TYR 0.012 0.001 TYR C 242 PHE 0.018 0.001 PHE E 205 TRP 0.031 0.001 TRP F 463 HIS 0.004 0.001 HIS F 431 Details of bonding type rmsd covalent geometry : bond 0.00279 (14115) covalent geometry : angle 0.51790 (19290) hydrogen bonds : bond 0.03479 ( 525) hydrogen bonds : angle 3.52818 ( 1503) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: A 352 ASN cc_start: 0.7224 (m110) cc_final: 0.6796 (t0) REVERT: A 397 GLN cc_start: 0.8145 (mt0) cc_final: 0.7546 (mm-40) REVERT: A 398 LYS cc_start: 0.6837 (mttt) cc_final: 0.6173 (mtpt) REVERT: A 472 TRP cc_start: 0.8002 (m-10) cc_final: 0.7120 (m-10) REVERT: B 208 LYS cc_start: 0.7421 (mmmt) cc_final: 0.6927 (mmmt) REVERT: E 244 LEU cc_start: 0.9118 (tp) cc_final: 0.8843 (tp) REVERT: E 357 ASN cc_start: 0.8574 (t0) cc_final: 0.7848 (t0) outliers start: 17 outliers final: 16 residues processed: 151 average time/residue: 0.1116 time to fit residues: 25.7008 Evaluate side-chains 148 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 457 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 457 GLU Chi-restraints excluded: chain F residue 421 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 52 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN B 309 HIS ** B 495 HIS ** 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 = 0.3530 r_free = 0.3530 target = 0.105344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.078827 restraints weight = 31597.818| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.01 r_work: 0.2962 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 14115 Z= 0.202 Angle : 0.591 13.124 19290 Z= 0.311 Chirality : 0.044 0.218 2205 Planarity : 0.004 0.048 2357 Dihedral : 9.871 157.165 2044 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.65 % Favored : 92.06 % Rotamer: Outliers : 1.10 % Allowed : 13.60 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.21), residues: 1713 helix: 1.61 (0.20), residues: 748 sheet: 0.64 (0.40), residues: 176 loop : -1.28 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 438 TYR 0.012 0.001 TYR A 264 PHE 0.019 0.001 PHE A 358 TRP 0.028 0.001 TRP F 463 HIS 0.014 0.001 HIS F 431 Details of bonding type rmsd covalent geometry : bond 0.00481 (14115) covalent geometry : angle 0.59100 (19290) hydrogen bonds : bond 0.04744 ( 525) hydrogen bonds : angle 3.83951 ( 1503) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 397 GLN cc_start: 0.8113 (mt0) cc_final: 0.7540 (mm-40) REVERT: A 398 LYS cc_start: 0.7006 (mttt) cc_final: 0.6346 (mtpt) REVERT: B 208 LYS cc_start: 0.7641 (mmmt) cc_final: 0.7046 (mmmt) REVERT: E 244 LEU cc_start: 0.9136 (tp) cc_final: 0.8848 (tp) REVERT: E 357 ASN cc_start: 0.8511 (t0) cc_final: 0.7806 (t0) outliers start: 16 outliers final: 16 residues processed: 146 average time/residue: 0.1176 time to fit residues: 26.7589 Evaluate side-chains 146 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 457 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 457 GLU Chi-restraints excluded: chain F residue 421 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 84 optimal weight: 0.6980 chunk 56 optimal weight: 0.0980 chunk 20 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 12 optimal weight: 0.0000 chunk 150 optimal weight: 0.7980 chunk 151 optimal weight: 7.9990 chunk 123 optimal weight: 0.0980 chunk 137 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 overall best weight: 0.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 309 HIS ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 HIS ** 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 = 0.3587 r_free = 0.3587 target = 0.108885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.082555 restraints weight = 31636.067| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.93 r_work: 0.3032 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 14115 Z= 0.100 Angle : 0.523 14.285 19290 Z= 0.275 Chirality : 0.041 0.192 2205 Planarity : 0.004 0.054 2357 Dihedral : 9.412 154.752 2044 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.95 % Favored : 93.75 % Rotamer: Outliers : 1.10 % Allowed : 13.94 % Favored : 84.96 % 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: 0.61 (0.21), residues: 1713 helix: 1.79 (0.20), residues: 743 sheet: 0.72 (0.40), residues: 186 loop : -1.08 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 438 TYR 0.011 0.001 TYR C 242 PHE 0.020 0.001 PHE E 205 TRP 0.055 0.001 TRP F 463 HIS 0.016 0.001 HIS F 431 Details of bonding type rmsd covalent geometry : bond 0.00221 (14115) covalent geometry : angle 0.52299 (19290) hydrogen bonds : bond 0.02930 ( 525) hydrogen bonds : angle 3.48286 ( 1503) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2927.51 seconds wall clock time: 51 minutes 12.94 seconds (3072.94 seconds total)