Starting phenix.real_space_refine on Mon May 4 01:48:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x94_38161/05_2026/8x94_38161.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x94_38161/05_2026/8x94_38161.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8x94_38161/05_2026/8x94_38161.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x94_38161/05_2026/8x94_38161.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x94_38161/05_2026/8x94_38161.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x94_38161/05_2026/8x94_38161.map" } resolution = 2.55 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= 0.009 sd= 0.120 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: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 11476 2.51 5 N 2784 2.21 5 O 3064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17444 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4310 Classifications: {'peptide': 531} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 517} Chain breaks: 1 Chain: "B" Number of atoms: 4310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4310 Classifications: {'peptide': 531} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 517} Chain breaks: 1 Chain: "C" Number of atoms: 4310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4310 Classifications: {'peptide': 531} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 517} Chain breaks: 1 Chain: "D" Number of atoms: 4310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4310 Classifications: {'peptide': 531} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 517} Chain breaks: 1 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'CLR': 1, 'EZI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'CLR': 1, 'EZI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'CLR': 1, 'EZI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'CLR': 1, 'EZI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.14, per 1000 atoms: 0.24 Number of scatterers: 17444 At special positions: 0 Unit cell: (124.95, 124.95, 112.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 3064 8.00 N 2784 7.00 C 11476 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: 1.18 Conformation dependent library (CDL) restraints added in 525.6 milliseconds 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4008 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 7 sheets defined 65.8% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 204 through 212 removed outlier: 3.990A pdb=" N ILE A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 225 removed outlier: 3.525A pdb=" N GLY A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 251 through 259 removed outlier: 3.652A pdb=" N ALA A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 271 removed outlier: 3.630A pdb=" N ASN A 271 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.560A pdb=" N ALA A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 321 removed outlier: 3.576A pdb=" N PHE A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 314 " --> pdb=" O TYR A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 344 Processing helix chain 'A' and resid 346 through 355 removed outlier: 3.665A pdb=" N TYR A 352 " --> pdb=" O GLY A 348 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 367 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 411 through 415 removed outlier: 3.852A pdb=" N LEU A 414 " --> pdb=" O HIS A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 430 removed outlier: 4.040A pdb=" N ARG A 421 " --> pdb=" O GLU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 455 removed outlier: 3.645A pdb=" N ILE A 434 " --> pdb=" O PHE A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 500 removed outlier: 3.518A pdb=" N ILE A 493 " --> pdb=" O PHE A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 531 removed outlier: 4.251A pdb=" N MET A 514 " --> pdb=" O SER A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 533 No H-bonds generated for 'chain 'A' and resid 532 through 533' Processing helix chain 'A' and resid 534 through 535 No H-bonds generated for 'chain 'A' and resid 534 through 535' Processing helix chain 'A' and resid 536 through 551 Processing helix chain 'A' and resid 552 through 557 removed outlier: 3.701A pdb=" N ARG A 557 " --> pdb=" O TYR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 576 Processing helix chain 'A' and resid 576 through 599 Processing helix chain 'A' and resid 630 through 640 Processing helix chain 'A' and resid 641 through 644 removed outlier: 3.620A pdb=" N GLY A 644 " --> pdb=" O PHE A 641 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 641 through 644' Processing helix chain 'A' and resid 656 through 672 Processing helix chain 'A' and resid 674 through 691 removed outlier: 3.654A pdb=" N ILE A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 685 " --> pdb=" O ALA A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 713 removed outlier: 3.536A pdb=" N ILE A 697 " --> pdb=" O GLU A 693 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A 699 " --> pdb=" O LYS A 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 212 removed outlier: 3.968A pdb=" N ILE B 208 " --> pdb=" O THR B 204 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 225 removed outlier: 3.546A pdb=" N LEU B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 Processing helix chain 'B' and resid 251 through 259 removed outlier: 3.558A pdb=" N ALA B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 271 removed outlier: 3.667A pdb=" N ASN B 271 " --> pdb=" O PHE B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 296 removed outlier: 3.514A pdb=" N VAL B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 321 removed outlier: 3.674A pdb=" N PHE B 305 " --> pdb=" O ASP B 301 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU B 312 " --> pdb=" O SER B 308 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 314 " --> pdb=" O TYR B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 329 removed outlier: 3.747A pdb=" N GLU B 328 " --> pdb=" O LYS B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 344 Processing helix chain 'B' and resid 346 through 355 removed outlier: 3.668A pdb=" N TYR B 352 " --> pdb=" O GLY B 348 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 367 Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 411 through 415 removed outlier: 3.871A pdb=" N LEU B 414 " --> pdb=" O HIS B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 430 removed outlier: 4.026A pdb=" N ARG B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 455 removed outlier: 3.624A pdb=" N ILE B 434 " --> pdb=" O PHE B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 500 Processing helix chain 'B' and resid 510 through 531 removed outlier: 4.201A pdb=" N MET B 514 " --> pdb=" O SER B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 533 No H-bonds generated for 'chain 'B' and resid 532 through 533' Processing helix chain 'B' and resid 534 through 535 No H-bonds generated for 'chain 'B' and resid 534 through 535' Processing helix chain 'B' and resid 536 through 551 Processing helix chain 'B' and resid 552 through 557 removed outlier: 3.701A pdb=" N ARG B 557 " --> pdb=" O TYR B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 576 Processing helix chain 'B' and resid 576 through 599 Processing helix chain 'B' and resid 630 through 640 Processing helix chain 'B' and resid 641 through 644 removed outlier: 3.602A pdb=" N GLY B 644 " --> pdb=" O PHE B 641 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 641 through 644' Processing helix chain 'B' and resid 656 through 672 Processing helix chain 'B' and resid 674 through 691 removed outlier: 3.611A pdb=" N ILE B 680 " --> pdb=" O LEU B 676 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 685 " --> pdb=" O ALA B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 713 removed outlier: 3.770A pdb=" N ILE B 697 " --> pdb=" O GLU B 693 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS B 699 " --> pdb=" O LYS B 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 212 removed outlier: 3.968A pdb=" N ILE C 208 " --> pdb=" O THR C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 224 Processing helix chain 'C' and resid 234 through 238 Processing helix chain 'C' and resid 251 through 259 removed outlier: 3.644A pdb=" N ALA C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 271 removed outlier: 3.593A pdb=" N ASN C 271 " --> pdb=" O PHE C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.555A pdb=" N ALA C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 321 removed outlier: 4.544A pdb=" N LYS C 304 " --> pdb=" O ALA C 300 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE C 305 " --> pdb=" O ASP C 301 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU C 312 " --> pdb=" O SER C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 344 Processing helix chain 'C' and resid 346 through 355 removed outlier: 3.673A pdb=" N TYR C 352 " --> pdb=" O GLY C 348 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN C 355 " --> pdb=" O ALA C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 367 Processing helix chain 'C' and resid 395 through 402 Processing helix chain 'C' and resid 411 through 415 removed outlier: 3.873A pdb=" N LEU C 414 " --> pdb=" O HIS C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 430 removed outlier: 4.051A pdb=" N ARG C 421 " --> pdb=" O GLU C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 455 removed outlier: 3.641A pdb=" N ILE C 434 " --> pdb=" O PHE C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 500 removed outlier: 3.533A pdb=" N ILE C 493 " --> pdb=" O PHE C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 531 removed outlier: 4.011A pdb=" N MET C 514 " --> pdb=" O SER C 510 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER C 520 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 527 " --> pdb=" O MET C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 533 No H-bonds generated for 'chain 'C' and resid 532 through 533' Processing helix chain 'C' and resid 534 through 535 No H-bonds generated for 'chain 'C' and resid 534 through 535' Processing helix chain 'C' and resid 536 through 551 removed outlier: 3.676A pdb=" N SER C 540 " --> pdb=" O GLU C 536 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 557 removed outlier: 3.701A pdb=" N ARG C 557 " --> pdb=" O TYR C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 576 Processing helix chain 'C' and resid 576 through 599 removed outlier: 3.532A pdb=" N PHE C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA C 594 " --> pdb=" O GLY C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 640 Processing helix chain 'C' and resid 641 through 644 removed outlier: 3.590A pdb=" N GLY C 644 " --> pdb=" O PHE C 641 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 641 through 644' Processing helix chain 'C' and resid 656 through 672 Processing helix chain 'C' and resid 674 through 691 removed outlier: 3.605A pdb=" N ILE C 680 " --> pdb=" O LEU C 676 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU C 685 " --> pdb=" O ALA C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 713 removed outlier: 3.945A pdb=" N ILE C 697 " --> pdb=" O GLU C 693 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS C 699 " --> pdb=" O LYS C 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 212 removed outlier: 4.034A pdb=" N ILE D 208 " --> pdb=" O THR D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 224 removed outlier: 3.514A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 238 Processing helix chain 'D' and resid 251 through 259 removed outlier: 3.657A pdb=" N ALA D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 270 Processing helix chain 'D' and resid 287 through 296 removed outlier: 3.558A pdb=" N ALA D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 321 removed outlier: 3.720A pdb=" N PHE D 305 " --> pdb=" O ASP D 301 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER D 308 " --> pdb=" O LYS D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 329 removed outlier: 3.598A pdb=" N GLU D 328 " --> pdb=" O LYS D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 344 Processing helix chain 'D' and resid 346 through 355 removed outlier: 3.703A pdb=" N TYR D 352 " --> pdb=" O GLY D 348 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN D 355 " --> pdb=" O ALA D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 367 Processing helix chain 'D' and resid 395 through 402 Processing helix chain 'D' and resid 411 through 415 removed outlier: 3.788A pdb=" N LEU D 414 " --> pdb=" O HIS D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 430 removed outlier: 4.050A pdb=" N ARG D 421 " --> pdb=" O GLU D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 455 removed outlier: 3.644A pdb=" N ILE D 434 " --> pdb=" O PHE D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 500 removed outlier: 3.524A pdb=" N ILE D 493 " --> pdb=" O PHE D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 531 removed outlier: 3.992A pdb=" N MET D 514 " --> pdb=" O SER D 510 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER D 520 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL D 527 " --> pdb=" O MET D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 551 removed outlier: 3.669A pdb=" N SER D 540 " --> pdb=" O GLU D 536 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 557 removed outlier: 3.694A pdb=" N ARG D 557 " --> pdb=" O TYR D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 576 Processing helix chain 'D' and resid 576 through 599 removed outlier: 3.586A pdb=" N PHE D 582 " --> pdb=" O CYS D 578 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA D 594 " --> pdb=" O GLY D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 640 Processing helix chain 'D' and resid 641 through 644 removed outlier: 3.578A pdb=" N GLY D 644 " --> pdb=" O PHE D 641 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 641 through 644' Processing helix chain 'D' and resid 656 through 672 Processing helix chain 'D' and resid 674 through 691 removed outlier: 3.672A pdb=" N ILE D 680 " --> pdb=" O LEU D 676 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU D 685 " --> pdb=" O ALA D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 713 removed outlier: 3.944A pdb=" N ILE D 697 " --> pdb=" O GLU D 693 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS D 699 " --> pdb=" O LYS D 695 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 369 through 374 removed outlier: 6.866A pdb=" N SER A 380 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ALA A 374 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A 747 " --> pdb=" O HIS A 379 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 725 through 728 removed outlier: 3.844A pdb=" N ARG A 740 " --> pdb=" O LEU A 727 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 371 through 374 removed outlier: 3.894A pdb=" N TRP B 373 " --> pdb=" O SER B 380 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 725 through 728 removed outlier: 3.500A pdb=" N LEU B 727 " --> pdb=" O ARG B 740 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG B 740 " --> pdb=" O LEU B 727 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 369 through 374 removed outlier: 6.905A pdb=" N SER C 380 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ALA C 374 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU C 747 " --> pdb=" O HIS C 379 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG C 740 " --> pdb=" O LEU C 727 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU C 727 " --> pdb=" O ARG C 740 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 369 through 374 removed outlier: 6.899A pdb=" N SER D 380 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ALA D 374 " --> pdb=" O VAL D 378 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL D 378 " --> pdb=" O ALA D 374 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 725 through 731 removed outlier: 3.845A pdb=" N ARG D 740 " --> pdb=" O LEU D 727 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL D 729 " --> pdb=" O ASP D 738 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ASP D 738 " --> pdb=" O VAL D 729 " (cutoff:3.500A) 936 hydrogen bonds defined for protein. 2697 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: 2.48 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 2684 1.27 - 1.40: 4792 1.40 - 1.54: 10023 1.54 - 1.68: 173 1.68 - 1.81: 204 Bond restraints: 17876 Sorted by residual: bond pdb=" C08 EZI D1201 " pdb=" C09 EZI D1201 " ideal model delta sigma weight residual 1.446 1.348 0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C08 EZI A1201 " pdb=" C09 EZI A1201 " ideal model delta sigma weight residual 1.446 1.349 0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" C08 EZI C1201 " pdb=" C09 EZI C1201 " ideal model delta sigma weight residual 1.446 1.350 0.096 2.00e-02 2.50e+03 2.33e+01 bond pdb=" C08 EZI B1201 " pdb=" C09 EZI B1201 " ideal model delta sigma weight residual 1.446 1.350 0.096 2.00e-02 2.50e+03 2.33e+01 bond pdb=" C22 EZI A1201 " pdb=" C23 EZI A1201 " ideal model delta sigma weight residual 1.428 1.523 -0.095 2.00e-02 2.50e+03 2.27e+01 ... (remaining 17871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 23899 2.22 - 4.44: 274 4.44 - 6.66: 32 6.66 - 8.88: 5 8.88 - 11.10: 6 Bond angle restraints: 24216 Sorted by residual: angle pdb=" C13 CLR C1202 " pdb=" C17 CLR C1202 " pdb=" C20 CLR C1202 " ideal model delta sigma weight residual 119.60 108.50 11.10 3.00e+00 1.11e-01 1.37e+01 angle pdb=" C13 CLR B1202 " pdb=" C17 CLR B1202 " pdb=" C20 CLR B1202 " ideal model delta sigma weight residual 119.60 108.50 11.10 3.00e+00 1.11e-01 1.37e+01 angle pdb=" C13 CLR A1202 " pdb=" C17 CLR A1202 " pdb=" C20 CLR A1202 " ideal model delta sigma weight residual 119.60 108.52 11.08 3.00e+00 1.11e-01 1.36e+01 angle pdb=" C13 CLR D1202 " pdb=" C17 CLR D1202 " pdb=" C20 CLR D1202 " ideal model delta sigma weight residual 119.60 108.57 11.03 3.00e+00 1.11e-01 1.35e+01 angle pdb=" N VAL C 228 " pdb=" CA VAL C 228 " pdb=" C VAL C 228 " ideal model delta sigma weight residual 113.39 108.16 5.23 1.47e+00 4.63e-01 1.27e+01 ... (remaining 24211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 9414 17.77 - 35.55: 976 35.55 - 53.32: 240 53.32 - 71.10: 37 71.10 - 88.87: 9 Dihedral angle restraints: 10676 sinusoidal: 4432 harmonic: 6244 Sorted by residual: dihedral pdb=" CA TYR A 654 " pdb=" C TYR A 654 " pdb=" N ASP A 655 " pdb=" CA ASP A 655 " ideal model delta harmonic sigma weight residual 180.00 156.07 23.93 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA TYR B 654 " pdb=" C TYR B 654 " pdb=" N ASP B 655 " pdb=" CA ASP B 655 " ideal model delta harmonic sigma weight residual 180.00 156.24 23.76 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA TYR C 654 " pdb=" C TYR C 654 " pdb=" N ASP C 655 " pdb=" CA ASP C 655 " ideal model delta harmonic sigma weight residual 180.00 156.32 23.68 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 10673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 2663 0.098 - 0.196: 41 0.196 - 0.294: 0 0.294 - 0.392: 8 0.392 - 0.490: 4 Chirality restraints: 2716 Sorted by residual: chirality pdb=" C17 CLR A1202 " pdb=" C13 CLR A1202 " pdb=" C16 CLR A1202 " pdb=" C20 CLR A1202 " both_signs ideal model delta sigma weight residual False 2.55 3.04 -0.49 2.00e-01 2.50e+01 5.99e+00 chirality pdb=" C17 CLR C1202 " pdb=" C13 CLR C1202 " pdb=" C16 CLR C1202 " pdb=" C20 CLR C1202 " both_signs ideal model delta sigma weight residual False 2.55 3.04 -0.49 2.00e-01 2.50e+01 5.97e+00 chirality pdb=" C17 CLR B1202 " pdb=" C13 CLR B1202 " pdb=" C16 CLR B1202 " pdb=" C20 CLR B1202 " both_signs ideal model delta sigma weight residual False 2.55 3.04 -0.49 2.00e-01 2.50e+01 5.90e+00 ... (remaining 2713 not shown) Planarity restraints: 2956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 360 " 0.061 5.00e-02 4.00e+02 9.18e-02 1.35e+01 pdb=" N PRO A 361 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO A 361 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 361 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 360 " 0.059 5.00e-02 4.00e+02 8.89e-02 1.27e+01 pdb=" N PRO B 361 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO B 361 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 361 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 360 " 0.046 5.00e-02 4.00e+02 6.96e-02 7.74e+00 pdb=" N PRO D 361 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO D 361 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 361 " 0.038 5.00e-02 4.00e+02 ... (remaining 2953 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3014 2.76 - 3.30: 16074 3.30 - 3.83: 26933 3.83 - 4.37: 32973 4.37 - 4.90: 55535 Nonbonded interactions: 134529 Sorted by model distance: nonbonded pdb=" O LEU D 255 " pdb=" OG1 THR D 259 " model vdw 2.227 3.040 nonbonded pdb=" O LEU B 255 " pdb=" OG1 THR B 259 " model vdw 2.239 3.040 nonbonded pdb=" O LEU C 255 " pdb=" OG1 THR C 259 " model vdw 2.248 3.040 nonbonded pdb=" O LYS A 304 " pdb=" OG SER A 308 " model vdw 2.258 3.040 nonbonded pdb=" O THR D 505 " pdb=" OG1 THR D 505 " model vdw 2.333 3.040 ... (remaining 134524 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.770 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 : 0.004 0.098 17876 Z= 0.209 Angle : 0.633 11.098 24216 Z= 0.331 Chirality : 0.045 0.490 2716 Planarity : 0.005 0.092 2956 Dihedral : 15.270 88.869 6668 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.16 % Allowed : 16.33 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.17), residues: 2108 helix: -0.39 (0.13), residues: 1204 sheet: -0.54 (0.60), residues: 76 loop : -1.34 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 421 TYR 0.010 0.001 TYR A 442 PHE 0.011 0.001 PHE B 370 TRP 0.008 0.001 TRP C 698 HIS 0.005 0.001 HIS B 411 Details of bonding type rmsd covalent geometry : bond 0.00429 (17876) covalent geometry : angle 0.63260 (24216) hydrogen bonds : bond 0.27964 ( 936) hydrogen bonds : angle 6.53684 ( 2697) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 166 time to evaluate : 0.447 Fit side-chains REVERT: A 645 MET cc_start: 0.8965 (mmp) cc_final: 0.8644 (mmm) REVERT: A 692 GLN cc_start: 0.6479 (mp10) cc_final: 0.6186 (pm20) REVERT: B 215 MET cc_start: 0.6131 (tmm) cc_final: 0.5489 (tmm) REVERT: B 465 LYS cc_start: 0.8152 (mmtm) cc_final: 0.7903 (mmpt) REVERT: B 717 MET cc_start: 0.2403 (pp-130) cc_final: 0.1843 (pmm) outliers start: 3 outliers final: 3 residues processed: 168 average time/residue: 0.6621 time to fit residues: 122.7014 Evaluate side-chains 162 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 159 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain D residue 514 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 379 HIS B 749 ASN C 224 ASN C 286 ASN C 411 HIS D 494 GLN D 498 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.211270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.139142 restraints weight = 16864.609| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.74 r_work: 0.3097 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17876 Z= 0.168 Angle : 0.594 9.538 24216 Z= 0.321 Chirality : 0.040 0.174 2716 Planarity : 0.004 0.061 2956 Dihedral : 5.856 57.577 2631 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.19 % Allowed : 15.36 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.18), residues: 2108 helix: 1.49 (0.14), residues: 1216 sheet: -0.93 (0.50), residues: 108 loop : -1.30 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 421 TYR 0.014 0.002 TYR C 584 PHE 0.011 0.002 PHE B 370 TRP 0.012 0.002 TRP C 698 HIS 0.003 0.001 HIS C 411 Details of bonding type rmsd covalent geometry : bond 0.00363 (17876) covalent geometry : angle 0.59392 (24216) hydrogen bonds : bond 0.08388 ( 936) hydrogen bonds : angle 4.02596 ( 2697) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 175 time to evaluate : 0.718 Fit side-chains REVERT: A 255 LEU cc_start: 0.5800 (OUTLIER) cc_final: 0.5491 (mm) REVERT: A 493 ILE cc_start: 0.7945 (pt) cc_final: 0.7717 (mt) REVERT: A 678 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8578 (ttm) REVERT: B 215 MET cc_start: 0.5953 (OUTLIER) cc_final: 0.5466 (tmm) REVERT: B 255 LEU cc_start: 0.5765 (OUTLIER) cc_final: 0.5505 (mm) REVERT: B 717 MET cc_start: 0.2975 (pp-130) cc_final: 0.2236 (ptt) REVERT: C 215 MET cc_start: 0.5846 (OUTLIER) cc_final: 0.5197 (tmm) REVERT: C 255 LEU cc_start: 0.5730 (OUTLIER) cc_final: 0.5445 (mm) REVERT: C 305 PHE cc_start: 0.5207 (OUTLIER) cc_final: 0.4953 (t80) REVERT: C 385 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7259 (mp) REVERT: C 493 ILE cc_start: 0.7970 (pt) cc_final: 0.7734 (mt) REVERT: D 478 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7852 (mt-10) REVERT: D 493 ILE cc_start: 0.7946 (pt) cc_final: 0.7681 (mt) REVERT: D 575 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6970 (ttm170) outliers start: 41 outliers final: 14 residues processed: 201 average time/residue: 0.6538 time to fit residues: 144.8834 Evaluate side-chains 183 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 514 MET Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 514 MET Chi-restraints excluded: chain D residue 575 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 130 optimal weight: 0.9980 chunk 185 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 69 optimal weight: 0.0010 chunk 92 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 112 optimal weight: 9.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 ASN B 420 ASN C 224 ASN C 420 ASN D 420 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.214858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.143714 restraints weight = 17255.919| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.81 r_work: 0.3163 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 17876 Z= 0.110 Angle : 0.480 8.189 24216 Z= 0.262 Chirality : 0.036 0.156 2716 Planarity : 0.003 0.051 2956 Dihedral : 5.373 58.425 2627 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.77 % Allowed : 17.51 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.19), residues: 2108 helix: 2.12 (0.14), residues: 1232 sheet: -0.70 (0.51), residues: 108 loop : -1.18 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 421 TYR 0.007 0.001 TYR C 310 PHE 0.009 0.001 PHE C 580 TRP 0.008 0.001 TRP C 698 HIS 0.004 0.001 HIS B 411 Details of bonding type rmsd covalent geometry : bond 0.00202 (17876) covalent geometry : angle 0.47991 (24216) hydrogen bonds : bond 0.05726 ( 936) hydrogen bonds : angle 3.64439 ( 2697) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 255 LEU cc_start: 0.5801 (OUTLIER) cc_final: 0.5500 (mm) REVERT: B 215 MET cc_start: 0.6018 (OUTLIER) cc_final: 0.5561 (tmm) REVERT: B 255 LEU cc_start: 0.5762 (OUTLIER) cc_final: 0.5474 (mm) REVERT: B 575 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6223 (mtt180) REVERT: B 717 MET cc_start: 0.2912 (pp-130) cc_final: 0.2110 (ptt) REVERT: C 215 MET cc_start: 0.6080 (OUTLIER) cc_final: 0.5468 (tmm) REVERT: C 255 LEU cc_start: 0.5689 (OUTLIER) cc_final: 0.5411 (mm) REVERT: C 328 GLU cc_start: 0.7937 (mp0) cc_final: 0.7538 (mp0) REVERT: D 215 MET cc_start: 0.5543 (tmm) cc_final: 0.5290 (tmm) REVERT: D 328 GLU cc_start: 0.7721 (mp0) cc_final: 0.7342 (mp0) outliers start: 33 outliers final: 10 residues processed: 189 average time/residue: 0.7123 time to fit residues: 147.6413 Evaluate side-chains 164 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 514 MET Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 732 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 14 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 148 optimal weight: 0.0970 chunk 115 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 224 ASN C 498 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.209613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.136205 restraints weight = 16914.889| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.76 r_work: 0.3077 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17876 Z= 0.176 Angle : 0.589 8.364 24216 Z= 0.317 Chirality : 0.040 0.159 2716 Planarity : 0.004 0.047 2956 Dihedral : 5.859 59.504 2624 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.16 % Allowed : 17.18 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.19), residues: 2108 helix: 1.94 (0.14), residues: 1228 sheet: -1.01 (0.49), residues: 108 loop : -1.37 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 421 TYR 0.015 0.002 TYR C 584 PHE 0.011 0.002 PHE A 650 TRP 0.013 0.002 TRP C 698 HIS 0.004 0.001 HIS D 411 Details of bonding type rmsd covalent geometry : bond 0.00393 (17876) covalent geometry : angle 0.58948 (24216) hydrogen bonds : bond 0.08481 ( 936) hydrogen bonds : angle 3.76729 ( 2697) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 161 time to evaluate : 0.668 Fit side-chains REVERT: A 199 TYR cc_start: 0.1681 (OUTLIER) cc_final: 0.0560 (m-80) REVERT: A 255 LEU cc_start: 0.5895 (OUTLIER) cc_final: 0.5605 (mm) REVERT: A 328 GLU cc_start: 0.7940 (mp0) cc_final: 0.7544 (mp0) REVERT: A 692 GLN cc_start: 0.6123 (mp10) cc_final: 0.5760 (pm20) REVERT: A 717 MET cc_start: 0.2339 (OUTLIER) cc_final: 0.1388 (mpp) REVERT: B 215 MET cc_start: 0.6207 (OUTLIER) cc_final: 0.5797 (tmm) REVERT: B 255 LEU cc_start: 0.6025 (OUTLIER) cc_final: 0.5720 (mm) REVERT: B 503 MET cc_start: 0.7270 (mmt) cc_final: 0.6970 (mmm) REVERT: B 575 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6298 (mtt180) REVERT: B 717 MET cc_start: 0.2765 (pp-130) cc_final: 0.2021 (ptt) REVERT: C 199 TYR cc_start: 0.1703 (OUTLIER) cc_final: 0.0556 (m-80) REVERT: C 215 MET cc_start: 0.6285 (OUTLIER) cc_final: 0.5781 (tmm) REVERT: C 255 LEU cc_start: 0.5795 (OUTLIER) cc_final: 0.5535 (mm) REVERT: C 503 MET cc_start: 0.7251 (mmt) cc_final: 0.6958 (mmm) REVERT: C 717 MET cc_start: 0.2347 (OUTLIER) cc_final: 0.1391 (mpp) REVERT: D 717 MET cc_start: 0.2092 (OUTLIER) cc_final: 0.1122 (mpp) outliers start: 59 outliers final: 21 residues processed: 199 average time/residue: 0.6568 time to fit residues: 144.1013 Evaluate side-chains 188 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 514 MET Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 693 GLU Chi-restraints excluded: chain D residue 717 MET Chi-restraints excluded: chain D residue 732 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 162 optimal weight: 30.0000 chunk 17 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 113 optimal weight: 0.1980 chunk 107 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 195 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 ASN B 420 ASN C 420 ASN D 420 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.210839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.137833 restraints weight = 16913.573| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.73 r_work: 0.3117 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17876 Z= 0.141 Angle : 0.535 7.665 24216 Z= 0.288 Chirality : 0.038 0.158 2716 Planarity : 0.004 0.044 2956 Dihedral : 5.667 59.246 2624 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.89 % Allowed : 17.51 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.19), residues: 2108 helix: 2.13 (0.14), residues: 1228 sheet: -1.14 (0.47), residues: 108 loop : -1.41 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 744 TYR 0.012 0.001 TYR C 584 PHE 0.010 0.001 PHE A 650 TRP 0.010 0.001 TRP B 698 HIS 0.004 0.001 HIS B 411 Details of bonding type rmsd covalent geometry : bond 0.00300 (17876) covalent geometry : angle 0.53460 (24216) hydrogen bonds : bond 0.07092 ( 936) hydrogen bonds : angle 3.61538 ( 2697) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 160 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 199 TYR cc_start: 0.1697 (OUTLIER) cc_final: 0.0550 (m-80) REVERT: A 320 LEU cc_start: 0.6222 (OUTLIER) cc_final: 0.5943 (mm) REVERT: A 328 GLU cc_start: 0.7826 (mp0) cc_final: 0.7419 (mp0) REVERT: A 678 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8669 (ttm) REVERT: A 692 GLN cc_start: 0.6053 (mp10) cc_final: 0.5746 (pm20) REVERT: A 717 MET cc_start: 0.2346 (OUTLIER) cc_final: 0.1345 (mpp) REVERT: B 199 TYR cc_start: 0.1669 (OUTLIER) cc_final: 0.0436 (m-80) REVERT: B 215 MET cc_start: 0.6219 (OUTLIER) cc_final: 0.5839 (tmm) REVERT: B 255 LEU cc_start: 0.5968 (OUTLIER) cc_final: 0.5673 (mm) REVERT: B 328 GLU cc_start: 0.7918 (mp0) cc_final: 0.7495 (mp0) REVERT: B 466 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.7625 (mmm) REVERT: B 503 MET cc_start: 0.7303 (mmt) cc_final: 0.7044 (mmm) REVERT: B 575 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.6310 (mtt180) REVERT: B 678 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8670 (ttm) REVERT: B 717 MET cc_start: 0.2738 (pp-130) cc_final: 0.1985 (ptt) REVERT: C 215 MET cc_start: 0.6407 (OUTLIER) cc_final: 0.5982 (tmm) REVERT: C 255 LEU cc_start: 0.5769 (OUTLIER) cc_final: 0.5493 (mm) REVERT: C 320 LEU cc_start: 0.5843 (OUTLIER) cc_final: 0.5429 (mm) REVERT: C 328 GLU cc_start: 0.7910 (mp0) cc_final: 0.7476 (mp0) REVERT: C 503 MET cc_start: 0.7249 (mmt) cc_final: 0.6967 (mmm) REVERT: C 717 MET cc_start: 0.2323 (OUTLIER) cc_final: 0.1323 (mpp) REVERT: D 215 MET cc_start: 0.5600 (tmm) cc_final: 0.5155 (mtp) REVERT: D 717 MET cc_start: 0.2119 (OUTLIER) cc_final: 0.1077 (mpp) REVERT: D 747 GLU cc_start: 0.5986 (OUTLIER) cc_final: 0.5058 (tp30) outliers start: 54 outliers final: 23 residues processed: 194 average time/residue: 0.6766 time to fit residues: 144.2702 Evaluate side-chains 194 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 514 MET Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 514 MET Chi-restraints excluded: chain D residue 693 GLU Chi-restraints excluded: chain D residue 717 MET Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 747 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 2 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 155 optimal weight: 0.0040 chunk 79 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 192 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 208 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.213173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.140386 restraints weight = 17013.591| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.71 r_work: 0.3172 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17876 Z= 0.112 Angle : 0.482 7.056 24216 Z= 0.262 Chirality : 0.036 0.154 2716 Planarity : 0.003 0.043 2956 Dihedral : 5.407 59.085 2624 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.41 % Allowed : 18.25 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.19), residues: 2108 helix: 2.38 (0.14), residues: 1232 sheet: -1.04 (0.48), residues: 108 loop : -1.33 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 744 TYR 0.008 0.001 TYR C 310 PHE 0.009 0.001 PHE C 580 TRP 0.009 0.001 TRP D 698 HIS 0.004 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00215 (17876) covalent geometry : angle 0.48191 (24216) hydrogen bonds : bond 0.05707 ( 936) hydrogen bonds : angle 3.46833 ( 2697) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 160 time to evaluate : 0.543 Fit side-chains REVERT: A 255 LEU cc_start: 0.6101 (OUTLIER) cc_final: 0.5785 (mm) REVERT: A 320 LEU cc_start: 0.6336 (OUTLIER) cc_final: 0.6048 (mm) REVERT: A 328 GLU cc_start: 0.7836 (mp0) cc_final: 0.7437 (mp0) REVERT: A 692 GLN cc_start: 0.5982 (mp10) cc_final: 0.5718 (pm20) REVERT: A 717 MET cc_start: 0.2461 (OUTLIER) cc_final: 0.1469 (mpp) REVERT: B 199 TYR cc_start: 0.1750 (OUTLIER) cc_final: 0.0486 (m-80) REVERT: B 215 MET cc_start: 0.6474 (OUTLIER) cc_final: 0.6183 (tmm) REVERT: B 320 LEU cc_start: 0.6195 (OUTLIER) cc_final: 0.5898 (mm) REVERT: B 328 GLU cc_start: 0.7809 (mp0) cc_final: 0.7416 (mp0) REVERT: B 466 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7597 (mmm) REVERT: B 499 ARG cc_start: 0.6580 (mmm160) cc_final: 0.6157 (tpp-160) REVERT: B 503 MET cc_start: 0.7304 (mmt) cc_final: 0.7070 (mmm) REVERT: B 575 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6263 (mtt180) REVERT: B 717 MET cc_start: 0.2468 (pp-130) cc_final: 0.1674 (ptt) REVERT: C 199 TYR cc_start: 0.1832 (OUTLIER) cc_final: 0.0638 (m-80) REVERT: C 215 MET cc_start: 0.6437 (OUTLIER) cc_final: 0.6067 (tmm) REVERT: C 255 LEU cc_start: 0.6039 (OUTLIER) cc_final: 0.5712 (mm) REVERT: C 320 LEU cc_start: 0.5809 (OUTLIER) cc_final: 0.5394 (mm) REVERT: C 328 GLU cc_start: 0.7818 (mp0) cc_final: 0.7388 (mp0) REVERT: C 503 MET cc_start: 0.7267 (mmt) cc_final: 0.7051 (mmm) REVERT: C 717 MET cc_start: 0.2196 (OUTLIER) cc_final: 0.1260 (mpp) REVERT: D 215 MET cc_start: 0.5690 (tmm) cc_final: 0.5134 (mtp) REVERT: D 747 GLU cc_start: 0.6013 (OUTLIER) cc_final: 0.5083 (tp30) outliers start: 45 outliers final: 19 residues processed: 189 average time/residue: 0.6930 time to fit residues: 144.3210 Evaluate side-chains 190 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 514 MET Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 514 MET Chi-restraints excluded: chain D residue 687 VAL Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 747 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 151 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 159 optimal weight: 50.0000 chunk 173 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 106 optimal weight: 50.0000 chunk 2 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN C 420 ASN D 311 ASN D 420 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.208468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.136111 restraints weight = 16873.867| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.71 r_work: 0.3064 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17876 Z= 0.189 Angle : 0.611 7.819 24216 Z= 0.327 Chirality : 0.042 0.181 2716 Planarity : 0.004 0.046 2956 Dihedral : 5.964 59.968 2624 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.69 % Allowed : 17.08 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.19), residues: 2108 helix: 1.99 (0.14), residues: 1220 sheet: -1.35 (0.46), residues: 108 loop : -1.38 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 744 TYR 0.016 0.002 TYR A 530 PHE 0.013 0.002 PHE A 650 TRP 0.014 0.002 TRP D 698 HIS 0.004 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00432 (17876) covalent geometry : angle 0.61094 (24216) hydrogen bonds : bond 0.08638 ( 936) hydrogen bonds : angle 3.71603 ( 2697) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 164 time to evaluate : 0.720 Fit side-chains REVERT: A 255 LEU cc_start: 0.6119 (OUTLIER) cc_final: 0.5825 (mm) REVERT: A 320 LEU cc_start: 0.6603 (OUTLIER) cc_final: 0.6157 (mm) REVERT: A 328 GLU cc_start: 0.7850 (mp0) cc_final: 0.7510 (mp0) REVERT: A 575 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.6787 (mpt-90) REVERT: A 692 GLN cc_start: 0.6198 (mp10) cc_final: 0.5928 (pm20) REVERT: A 717 MET cc_start: 0.2534 (OUTLIER) cc_final: 0.1384 (mpp) REVERT: A 747 GLU cc_start: 0.5853 (OUTLIER) cc_final: 0.4947 (tp30) REVERT: B 199 TYR cc_start: 0.1777 (OUTLIER) cc_final: 0.0507 (m-80) REVERT: B 215 MET cc_start: 0.6442 (OUTLIER) cc_final: 0.6143 (tmm) REVERT: B 255 LEU cc_start: 0.6101 (OUTLIER) cc_final: 0.5818 (mm) REVERT: B 320 LEU cc_start: 0.6343 (OUTLIER) cc_final: 0.6004 (mm) REVERT: B 330 THR cc_start: 0.7208 (OUTLIER) cc_final: 0.6818 (t) REVERT: B 466 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7719 (mmm) REVERT: B 503 MET cc_start: 0.7273 (mmt) cc_final: 0.7009 (mmm) REVERT: B 575 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6295 (mtt180) REVERT: B 717 MET cc_start: 0.2447 (pp-130) cc_final: 0.1510 (pmt) REVERT: C 215 MET cc_start: 0.6575 (OUTLIER) cc_final: 0.6241 (tmm) REVERT: C 255 LEU cc_start: 0.6029 (OUTLIER) cc_final: 0.5724 (mm) REVERT: C 320 LEU cc_start: 0.5871 (OUTLIER) cc_final: 0.5434 (mm) REVERT: C 328 GLU cc_start: 0.7884 (mp0) cc_final: 0.7459 (mp0) REVERT: C 466 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.7813 (mmm) REVERT: C 503 MET cc_start: 0.7242 (mmt) cc_final: 0.6979 (mmm) REVERT: C 717 MET cc_start: 0.2447 (OUTLIER) cc_final: 0.1352 (mpp) REVERT: C 747 GLU cc_start: 0.6001 (OUTLIER) cc_final: 0.5035 (tp30) REVERT: D 215 MET cc_start: 0.5694 (tmm) cc_final: 0.5181 (mtp) REVERT: D 575 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6950 (ttm170) REVERT: D 717 MET cc_start: 0.2296 (OUTLIER) cc_final: 0.1057 (mpp) REVERT: D 747 GLU cc_start: 0.5874 (OUTLIER) cc_final: 0.5003 (tp30) outliers start: 69 outliers final: 30 residues processed: 210 average time/residue: 0.6989 time to fit residues: 161.1450 Evaluate side-chains 213 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 162 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 575 ARG Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 514 MET Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 747 GLU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 514 MET Chi-restraints excluded: chain D residue 575 ARG Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 693 GLU Chi-restraints excluded: chain D residue 717 MET Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 747 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 86 optimal weight: 4.9990 chunk 169 optimal weight: 7.9990 chunk 156 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 125 optimal weight: 20.0000 chunk 41 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 420 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.209772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.136426 restraints weight = 16910.400| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.70 r_work: 0.3113 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17876 Z= 0.150 Angle : 0.551 7.164 24216 Z= 0.296 Chirality : 0.039 0.158 2716 Planarity : 0.004 0.041 2956 Dihedral : 5.768 59.835 2624 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.10 % Allowed : 17.67 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.19), residues: 2108 helix: 2.15 (0.14), residues: 1220 sheet: -1.39 (0.46), residues: 108 loop : -1.44 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 744 TYR 0.013 0.002 TYR C 584 PHE 0.010 0.002 PHE A 650 TRP 0.011 0.001 TRP D 698 HIS 0.004 0.001 HIS D 411 Details of bonding type rmsd covalent geometry : bond 0.00324 (17876) covalent geometry : angle 0.55056 (24216) hydrogen bonds : bond 0.07343 ( 936) hydrogen bonds : angle 3.60984 ( 2697) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 165 time to evaluate : 0.647 Fit side-chains REVERT: A 255 LEU cc_start: 0.6072 (OUTLIER) cc_final: 0.5784 (mm) REVERT: A 320 LEU cc_start: 0.6578 (OUTLIER) cc_final: 0.6145 (mm) REVERT: A 328 GLU cc_start: 0.7830 (mp0) cc_final: 0.7459 (mp0) REVERT: A 692 GLN cc_start: 0.6126 (mp10) cc_final: 0.5859 (pm20) REVERT: A 717 MET cc_start: 0.2504 (OUTLIER) cc_final: 0.1379 (mpp) REVERT: B 199 TYR cc_start: 0.1775 (OUTLIER) cc_final: 0.0506 (m-80) REVERT: B 215 MET cc_start: 0.6539 (OUTLIER) cc_final: 0.6259 (tmm) REVERT: B 255 LEU cc_start: 0.6036 (OUTLIER) cc_final: 0.5748 (mm) REVERT: B 320 LEU cc_start: 0.6329 (OUTLIER) cc_final: 0.5996 (mm) REVERT: B 328 GLU cc_start: 0.7876 (mp0) cc_final: 0.7495 (mp0) REVERT: B 330 THR cc_start: 0.7212 (OUTLIER) cc_final: 0.6832 (t) REVERT: B 466 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7637 (mmm) REVERT: B 503 MET cc_start: 0.7219 (mmt) cc_final: 0.6961 (mmm) REVERT: B 575 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.6334 (mtt180) REVERT: B 717 MET cc_start: 0.2474 (pp-130) cc_final: 0.1545 (pmt) REVERT: C 215 MET cc_start: 0.6553 (OUTLIER) cc_final: 0.6268 (tmm) REVERT: C 255 LEU cc_start: 0.6053 (OUTLIER) cc_final: 0.5745 (mm) REVERT: C 320 LEU cc_start: 0.5936 (OUTLIER) cc_final: 0.5451 (mm) REVERT: C 328 GLU cc_start: 0.7871 (mp0) cc_final: 0.7435 (mp0) REVERT: C 503 MET cc_start: 0.7216 (mmt) cc_final: 0.6963 (mmm) REVERT: C 717 MET cc_start: 0.2452 (OUTLIER) cc_final: 0.1372 (mpp) REVERT: C 747 GLU cc_start: 0.5960 (OUTLIER) cc_final: 0.5021 (tp30) REVERT: D 215 MET cc_start: 0.5612 (tmm) cc_final: 0.5115 (mtp) REVERT: D 294 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6532 (tp30) REVERT: D 305 PHE cc_start: 0.5208 (t80) cc_final: 0.4842 (t80) REVERT: D 575 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.6676 (ttm170) REVERT: D 747 GLU cc_start: 0.5879 (OUTLIER) cc_final: 0.4990 (tp30) outliers start: 58 outliers final: 26 residues processed: 203 average time/residue: 0.7084 time to fit residues: 157.7186 Evaluate side-chains 207 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 163 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 514 MET Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 747 GLU Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 514 MET Chi-restraints excluded: chain D residue 575 ARG Chi-restraints excluded: chain D residue 687 VAL Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 747 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 13 optimal weight: 6.9990 chunk 201 optimal weight: 0.1980 chunk 79 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 203 optimal weight: 1.9990 chunk 106 optimal weight: 50.0000 chunk 4 optimal weight: 0.5980 chunk 202 optimal weight: 0.9980 chunk 176 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN C 420 ASN D 420 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.214421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.142774 restraints weight = 17255.195| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.71 r_work: 0.3196 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17876 Z= 0.107 Angle : 0.470 6.538 24216 Z= 0.257 Chirality : 0.036 0.153 2716 Planarity : 0.003 0.038 2956 Dihedral : 5.271 57.127 2624 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.82 % Allowed : 18.95 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.19), residues: 2108 helix: 2.51 (0.15), residues: 1224 sheet: -1.19 (0.46), residues: 108 loop : -1.45 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 744 TYR 0.009 0.001 TYR D 530 PHE 0.009 0.001 PHE C 650 TRP 0.009 0.001 TRP D 698 HIS 0.005 0.001 HIS D 411 Details of bonding type rmsd covalent geometry : bond 0.00203 (17876) covalent geometry : angle 0.46996 (24216) hydrogen bonds : bond 0.05050 ( 936) hydrogen bonds : angle 3.40965 ( 2697) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 0.604 Fit side-chains REVERT: A 255 LEU cc_start: 0.5981 (OUTLIER) cc_final: 0.5735 (mm) REVERT: A 320 LEU cc_start: 0.6611 (OUTLIER) cc_final: 0.6126 (mm) REVERT: A 328 GLU cc_start: 0.7850 (mp0) cc_final: 0.7501 (mp0) REVERT: A 678 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8365 (ttp) REVERT: A 692 GLN cc_start: 0.5941 (mp10) cc_final: 0.5632 (pm20) REVERT: B 199 TYR cc_start: 0.1896 (OUTLIER) cc_final: 0.0592 (m-80) REVERT: B 215 MET cc_start: 0.6589 (OUTLIER) cc_final: 0.6305 (mmm) REVERT: B 255 LEU cc_start: 0.5990 (OUTLIER) cc_final: 0.5687 (mm) REVERT: B 320 LEU cc_start: 0.6378 (OUTLIER) cc_final: 0.5996 (mm) REVERT: B 328 GLU cc_start: 0.7875 (mp0) cc_final: 0.7524 (mp0) REVERT: B 466 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7602 (mmm) REVERT: B 499 ARG cc_start: 0.6541 (mmm160) cc_final: 0.6115 (tpp-160) REVERT: B 503 MET cc_start: 0.7206 (mmt) cc_final: 0.6966 (mmm) REVERT: B 575 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.6200 (mtt180) REVERT: B 717 MET cc_start: 0.2374 (pp-130) cc_final: 0.1595 (ptt) REVERT: C 215 MET cc_start: 0.6637 (OUTLIER) cc_final: 0.6383 (tmm) REVERT: C 255 LEU cc_start: 0.6025 (OUTLIER) cc_final: 0.5728 (mm) REVERT: C 320 LEU cc_start: 0.5795 (OUTLIER) cc_final: 0.5343 (mm) REVERT: C 328 GLU cc_start: 0.7860 (mp0) cc_final: 0.7468 (mp0) REVERT: C 503 MET cc_start: 0.7161 (mmt) cc_final: 0.6932 (mmm) REVERT: C 747 GLU cc_start: 0.6071 (OUTLIER) cc_final: 0.5140 (tp30) REVERT: D 215 MET cc_start: 0.5678 (tmm) cc_final: 0.5172 (mtp) REVERT: D 575 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6589 (ttm170) REVERT: D 747 GLU cc_start: 0.5875 (OUTLIER) cc_final: 0.4938 (tp30) outliers start: 34 outliers final: 17 residues processed: 180 average time/residue: 0.6874 time to fit residues: 136.2090 Evaluate side-chains 189 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 514 MET Chi-restraints excluded: chain C residue 747 GLU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 514 MET Chi-restraints excluded: chain D residue 575 ARG Chi-restraints excluded: chain D residue 747 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 16 optimal weight: 0.2980 chunk 119 optimal weight: 0.0070 chunk 20 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 142 optimal weight: 7.9990 chunk 208 optimal weight: 10.0000 chunk 200 optimal weight: 2.9990 chunk 54 optimal weight: 30.0000 chunk 4 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 overall best weight: 1.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.211324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.146928 restraints weight = 17166.423| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.07 r_work: 0.3090 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17876 Z= 0.118 Angle : 0.493 6.787 24216 Z= 0.267 Chirality : 0.037 0.150 2716 Planarity : 0.003 0.049 2956 Dihedral : 5.427 58.714 2624 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.98 % Allowed : 19.11 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.19), residues: 2108 helix: 2.51 (0.14), residues: 1224 sheet: -1.09 (0.46), residues: 108 loop : -1.43 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 744 TYR 0.009 0.001 TYR A 200 PHE 0.009 0.001 PHE C 580 TRP 0.010 0.001 TRP D 698 HIS 0.005 0.001 HIS D 411 Details of bonding type rmsd covalent geometry : bond 0.00233 (17876) covalent geometry : angle 0.49276 (24216) hydrogen bonds : bond 0.05905 ( 936) hydrogen bonds : angle 3.43594 ( 2697) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 163 time to evaluate : 0.656 Fit side-chains REVERT: A 255 LEU cc_start: 0.6039 (OUTLIER) cc_final: 0.5809 (mm) REVERT: A 320 LEU cc_start: 0.6733 (OUTLIER) cc_final: 0.6211 (mm) REVERT: A 328 GLU cc_start: 0.7979 (mp0) cc_final: 0.7643 (mp0) REVERT: A 678 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8622 (ttm) REVERT: A 692 GLN cc_start: 0.6219 (mp10) cc_final: 0.5978 (pm20) REVERT: A 747 GLU cc_start: 0.5891 (OUTLIER) cc_final: 0.4952 (tp30) REVERT: B 199 TYR cc_start: 0.1909 (OUTLIER) cc_final: 0.0590 (m-80) REVERT: B 215 MET cc_start: 0.6669 (OUTLIER) cc_final: 0.6410 (mmm) REVERT: B 255 LEU cc_start: 0.6016 (OUTLIER) cc_final: 0.5726 (mm) REVERT: B 320 LEU cc_start: 0.6489 (OUTLIER) cc_final: 0.6088 (mm) REVERT: B 328 GLU cc_start: 0.7971 (mp0) cc_final: 0.7618 (mp0) REVERT: B 466 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7730 (mmm) REVERT: B 499 ARG cc_start: 0.6721 (mmm160) cc_final: 0.6300 (tpp-160) REVERT: B 503 MET cc_start: 0.7211 (mmt) cc_final: 0.6975 (mmm) REVERT: B 575 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.6406 (mtt180) REVERT: B 717 MET cc_start: 0.2386 (pp-130) cc_final: 0.1617 (ptt) REVERT: C 215 MET cc_start: 0.6586 (OUTLIER) cc_final: 0.6359 (tmm) REVERT: C 320 LEU cc_start: 0.5943 (OUTLIER) cc_final: 0.5538 (mm) REVERT: C 328 GLU cc_start: 0.7941 (mp0) cc_final: 0.7600 (mp0) REVERT: C 503 MET cc_start: 0.7234 (mmt) cc_final: 0.6990 (mmm) REVERT: C 747 GLU cc_start: 0.6059 (OUTLIER) cc_final: 0.5093 (tp30) REVERT: D 215 MET cc_start: 0.5705 (tmm) cc_final: 0.5148 (mtp) REVERT: D 575 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.6645 (ttm170) REVERT: D 747 GLU cc_start: 0.6028 (OUTLIER) cc_final: 0.5083 (tp30) outliers start: 37 outliers final: 21 residues processed: 184 average time/residue: 0.7184 time to fit residues: 144.9343 Evaluate side-chains 197 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 514 MET Chi-restraints excluded: chain C residue 747 GLU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 514 MET Chi-restraints excluded: chain D residue 575 ARG Chi-restraints excluded: chain D residue 687 VAL Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 747 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 8 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 162 optimal weight: 30.0000 chunk 140 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.209204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.145328 restraints weight = 17161.673| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.06 r_work: 0.3056 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17876 Z= 0.141 Angle : 0.536 7.912 24216 Z= 0.288 Chirality : 0.038 0.150 2716 Planarity : 0.004 0.056 2956 Dihedral : 5.680 59.924 2624 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.36 % Allowed : 19.00 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.19), residues: 2108 helix: 2.37 (0.14), residues: 1224 sheet: -1.19 (0.45), residues: 108 loop : -1.52 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 744 TYR 0.011 0.001 TYR B 530 PHE 0.009 0.001 PHE A 650 TRP 0.011 0.001 TRP C 698 HIS 0.005 0.001 HIS D 411 Details of bonding type rmsd covalent geometry : bond 0.00299 (17876) covalent geometry : angle 0.53592 (24216) hydrogen bonds : bond 0.07036 ( 936) hydrogen bonds : angle 3.55050 ( 2697) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7636.10 seconds wall clock time: 130 minutes 10.18 seconds (7810.18 seconds total)