Starting phenix.real_space_refine on Thu Jul 2 13:12:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hbh_34632/07_2026/8hbh_34632.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hbh_34632/07_2026/8hbh_34632.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hbh_34632/07_2026/8hbh_34632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hbh_34632/07_2026/8hbh_34632.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hbh_34632/07_2026/8hbh_34632.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hbh_34632/07_2026/8hbh_34632.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hbh_34632/07_2026/8hbh_34632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hbh_34632/07_2026/8hbh_34632.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.158 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: 7 Type Number sf(0) Gaussians Fe 1 7.16 5 P 3 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 5469 2.51 5 N 1455 2.21 5 O 1514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8502 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 3922 Classifications: {'peptide': 522} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 24, 'TRANS': 497} Chain breaks: 9 Unresolved non-hydrogen bonds: 211 Unresolved non-hydrogen angles: 262 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 14, 'ASN:plan1': 3, 'GLN:plan1': 3, 'PHE:plan': 2, 'ASP:plan': 8, 'ARG:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 148 Chain: "B" Number of atoms: 4501 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 577, 4492 Classifications: {'peptide': 577} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 553} Chain breaks: 2 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 90 Planarities with less than four sites: {'GLU:plan': 19, 'ASP:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 96 Conformer: "B" Number of residues, atoms: 577, 4492 Classifications: {'peptide': 577} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 553} Chain breaks: 2 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 90 Planarities with less than four sites: {'GLU:plan': 19, 'ASP:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 96 bond proxies already assigned to first conformer: 4572 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {' NO': 1, 'G2P': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LEU A 254 " occ=0.80 ... (3 atoms not shown) pdb=" CB LEU A 254 " occ=0.80 Time building chain proxies: 2.17, per 1000 atoms: 0.26 Number of scatterers: 8502 At special positions: 0 Unit cell: (71.06, 107.635, 150.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 1 26.01 S 58 16.00 P 3 15.00 Mg 2 11.99 O 1514 8.00 N 1455 7.00 C 5469 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 420.4 milliseconds 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2070 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 8 sheets defined 49.4% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 70 through 83 Processing helix chain 'A' and resid 85 through 99 Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 130 through 149 removed outlier: 3.675A pdb=" N LEU A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU A 147 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP A 148 " --> pdb=" O CYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 removed outlier: 3.838A pdb=" N VAL A 155 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 171 removed outlier: 3.548A pdb=" N PHE A 166 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N SER A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N THR A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 227 removed outlier: 4.073A pdb=" N ILE A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) Proline residue: A 216 - end of helix removed outlier: 3.783A pdb=" N LYS A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 286 Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 319 through 323 removed outlier: 3.690A pdb=" N TYR A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 319 through 323' Processing helix chain 'A' and resid 334 through 341 removed outlier: 3.871A pdb=" N MET A 341 " --> pdb=" O GLY A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 407 Processing helix chain 'A' and resid 408 through 458 removed outlier: 3.778A pdb=" N VAL A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN A 441 " --> pdb=" O GLU A 437 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU A 444 " --> pdb=" O HIS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 468 removed outlier: 3.599A pdb=" N GLN A 468 " --> pdb=" O GLN A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 497 removed outlier: 3.553A pdb=" N ILE A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 519 removed outlier: 3.585A pdb=" N GLN A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU A 519 " --> pdb=" O GLN A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 560 Processing helix chain 'A' and resid 598 through 610 removed outlier: 3.710A pdb=" N THR A 602 " --> pdb=" O GLY A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 627 Processing helix chain 'B' and resid 2 through 18 removed outlier: 4.346A pdb=" N ASN B 6 " --> pdb=" O TYR B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 29 Processing helix chain 'B' and resid 44 through 60 removed outlier: 3.826A pdb=" N THR B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 82 Processing helix chain 'B' and resid 83 through 91 removed outlier: 3.560A pdb=" N LEU B 87 " --> pdb=" O TYR B 83 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 90 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLY B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 112 removed outlier: 4.764A pdb=" N ASP B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ALA B 103 " --> pdb=" O GLN B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 157 Processing helix chain 'B' and resid 209 through 217 Processing helix chain 'B' and resid 233 through 240 Processing helix chain 'B' and resid 241 through 244 Processing helix chain 'B' and resid 249 through 252 Processing helix chain 'B' and resid 264 through 271 removed outlier: 3.828A pdb=" N HIS B 271 " --> pdb=" O GLY B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 336 Processing helix chain 'B' and resid 348 through 398 removed outlier: 4.005A pdb=" N LEU B 354 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 408 removed outlier: 3.879A pdb=" N HIS B 408 " --> pdb=" O ASN B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 437 Processing helix chain 'B' and resid 443 through 463 removed outlier: 3.938A pdb=" N VAL B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER B 463 " --> pdb=" O THR B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 507 removed outlier: 3.869A pdb=" N SER B 495 " --> pdb=" O HIS B 491 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE B 496 " --> pdb=" O HIS B 492 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N CYS B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 556 removed outlier: 3.884A pdb=" N ASN B 548 " --> pdb=" O GLY B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 573 Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 204 Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 301 removed outlier: 6.714A pdb=" N MET A 291 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE A 301 " --> pdb=" O HIS A 289 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N HIS A 289 " --> pdb=" O PHE A 301 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 523 through 528 removed outlier: 7.199A pdb=" N CYS A 533 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR A 527 " --> pdb=" O ALA A 531 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA A 531 " --> pdb=" O THR A 527 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LYS A 476 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA A 584 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N SER A 478 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL A 582 " --> pdb=" O SER A 478 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 523 through 528 removed outlier: 7.199A pdb=" N CYS A 533 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR A 527 " --> pdb=" O ALA A 531 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA A 531 " --> pdb=" O THR A 527 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LYS A 476 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA A 584 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N SER A 478 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL A 582 " --> pdb=" O SER A 478 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N MET A 573 " --> pdb=" O LYS A 615 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ASN A 617 " --> pdb=" O MET A 573 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE A 575 " --> pdb=" O ASN A 617 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILE A 616 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N CYS A 654 " --> pdb=" O ARG A 637 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A 637 " --> pdb=" O CYS A 654 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 119 through 123 removed outlier: 6.323A pdb=" N LEU B 180 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N VAL B 166 " --> pdb=" O LEU B 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.811A pdb=" N ILE B 222 " --> pdb=" O THR B 230 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N CYS B 232 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N HIS B 220 " --> pdb=" O CYS B 232 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 318 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL B 277 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 469 through 475 removed outlier: 7.097A pdb=" N MET B 480 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR B 474 " --> pdb=" O LYS B 478 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LYS B 478 " --> pdb=" O THR B 474 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B 421 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ARG B 416 " --> pdb=" O THR B 530 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR B 530 " --> pdb=" O ARG B 416 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ASP B 418 " --> pdb=" O VAL B 528 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL B 528 " --> pdb=" O ASP B 418 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 469 through 475 removed outlier: 7.097A pdb=" N MET B 480 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR B 474 " --> pdb=" O LYS B 478 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LYS B 478 " --> pdb=" O THR B 474 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B 421 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ARG B 416 " --> pdb=" O THR B 530 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR B 530 " --> pdb=" O ARG B 416 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ASP B 418 " --> pdb=" O VAL B 528 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL B 528 " --> pdb=" O ASP B 418 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N ASN B 563 " --> pdb=" O ILE B 519 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE B 521 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N SER B 565 " --> pdb=" O ILE B 521 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE B 523 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE B 562 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N MET B 599 " --> pdb=" O PRO B 589 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL B 601 " --> pdb=" O ARG B 587 " (cutoff:3.500A) 498 hydrogen bonds defined for protein. 1433 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: 1.05 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 3346 1.38 - 1.56: 5227 1.56 - 1.74: 5 1.74 - 1.92: 92 1.92 - 2.09: 3 Bond restraints: 8673 Sorted by residual: bond pdb=" O3B G2P B1001 " pdb=" PG G2P B1001 " ideal model delta sigma weight residual 1.716 1.604 0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" O1A G2P B1001 " pdb=" PA G2P B1001 " ideal model delta sigma weight residual 1.507 1.606 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" O1B G2P B1001 " pdb=" PB G2P B1001 " ideal model delta sigma weight residual 1.510 1.607 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C3C HEM B1002 " pdb=" CAC HEM B1002 " ideal model delta sigma weight residual 1.544 1.456 0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" C3B HEM B1002 " pdb=" CAB HEM B1002 " ideal model delta sigma weight residual 1.544 1.462 0.082 2.00e-02 2.50e+03 1.67e+01 ... (remaining 8668 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 11571 2.79 - 5.58: 167 5.58 - 8.37: 24 8.37 - 11.15: 6 11.15 - 13.94: 2 Bond angle restraints: 11770 Sorted by residual: angle pdb=" N VAL A 363 " pdb=" CA VAL A 363 " pdb=" C VAL A 363 " ideal model delta sigma weight residual 110.42 118.52 -8.10 9.60e-01 1.09e+00 7.11e+01 angle pdb=" N PHE A 682 " pdb=" CA PHE A 682 " pdb=" C PHE A 682 " ideal model delta sigma weight residual 114.31 122.19 -7.88 1.29e+00 6.01e-01 3.74e+01 angle pdb=" N MET A 364 " pdb=" CA MET A 364 " pdb=" C MET A 364 " ideal model delta sigma weight residual 108.60 116.86 -8.26 1.46e+00 4.69e-01 3.20e+01 angle pdb=" PA G2P B1001 " pdb=" C3A G2P B1001 " pdb=" PB G2P B1001 " ideal model delta sigma weight residual 120.83 106.89 13.94 3.00e+00 1.11e-01 2.16e+01 angle pdb=" N MET B 164 " pdb=" CA MET B 164 " pdb=" C MET B 164 " ideal model delta sigma weight residual 107.41 116.09 -8.68 2.02e+00 2.45e-01 1.85e+01 ... (remaining 11765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.32: 4499 16.32 - 32.63: 519 32.63 - 48.95: 128 48.95 - 65.26: 31 65.26 - 81.58: 3 Dihedral angle restraints: 5180 sinusoidal: 1986 harmonic: 3194 Sorted by residual: dihedral pdb=" CA ARG B 407 " pdb=" C ARG B 407 " pdb=" N HIS B 408 " pdb=" CA HIS B 408 " ideal model delta harmonic sigma weight residual 180.00 158.53 21.47 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA HIS A 406 " pdb=" C HIS A 406 " pdb=" N ASN A 407 " pdb=" CA ASN A 407 " ideal model delta harmonic sigma weight residual -180.00 -158.62 -21.38 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" C VAL A 363 " pdb=" N VAL A 363 " pdb=" CA VAL A 363 " pdb=" CB VAL A 363 " ideal model delta harmonic sigma weight residual -122.00 -132.68 10.68 0 2.50e+00 1.60e-01 1.82e+01 ... (remaining 5177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1199 0.075 - 0.150: 159 0.150 - 0.226: 7 0.226 - 0.301: 2 0.301 - 0.376: 4 Chirality restraints: 1371 Sorted by residual: chirality pdb=" CA VAL A 363 " pdb=" N VAL A 363 " pdb=" C VAL A 363 " pdb=" CB VAL A 363 " both_signs ideal model delta sigma weight residual False 2.44 2.07 0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CA MET A 364 " pdb=" N MET A 364 " pdb=" C MET A 364 " pdb=" CB MET A 364 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CA ASP A 521 " pdb=" N ASP A 521 " pdb=" C ASP A 521 " pdb=" CB ASP A 521 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.72e+00 ... (remaining 1368 not shown) Planarity restraints: 1477 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 467 " 0.021 2.00e-02 2.50e+03 1.63e-02 6.62e+00 pdb=" CG TRP A 467 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP A 467 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 467 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 467 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 467 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 467 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 467 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 467 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 467 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 161 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.53e+00 pdb=" C GLU B 161 " 0.037 2.00e-02 2.50e+03 pdb=" O GLU B 161 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE B 162 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 519 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.27e+00 pdb=" C GLU A 519 " -0.031 2.00e-02 2.50e+03 pdb=" O GLU A 519 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU A 520 " 0.011 2.00e-02 2.50e+03 ... (remaining 1474 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 71 2.59 - 3.16: 6947 3.16 - 3.74: 12958 3.74 - 4.32: 18268 4.32 - 4.90: 31280 Nonbonded interactions: 69524 Sorted by model distance: nonbonded pdb=" OD2 ASP A 530 " pdb="MG MG A 701 " model vdw 2.007 2.170 nonbonded pdb=" O ILE A 487 " pdb="MG MG A 702 " model vdw 2.221 2.170 nonbonded pdb=" O ILE A 82 " pdb=" OG1 THR A 211 " model vdw 2.241 3.040 nonbonded pdb=" OH TYR B 395 " pdb=" OD1 ASN B 404 " model vdw 2.244 3.040 nonbonded pdb=" O LEU B 251 " pdb=" NZ LYS B 281 " model vdw 2.250 3.120 ... (remaining 69519 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.010 Normalize map: mean=0, sd=1: 1.020 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: 0.020 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.790 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.411 8674 Z= 0.344 Angle : 0.840 13.942 11770 Z= 0.423 Chirality : 0.052 0.376 1371 Planarity : 0.005 0.061 1477 Dihedral : 15.082 81.578 3110 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.90 % Allowed : 20.43 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.10 (0.25), residues: 1074 helix: 0.57 (0.23), residues: 501 sheet: 0.10 (0.34), residues: 221 loop : -0.95 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 335 TYR 0.017 0.002 TYR B 237 PHE 0.021 0.002 PHE A 682 TRP 0.045 0.003 TRP A 467 HIS 0.008 0.001 HIS A 539 Details of bonding type rmsd/Z covalent geometry : bond 0.00755 / 0.34 ( 8673) covalent geometry : angle 0.83959 / 0.42 (11770) hydrogen bonds : bond 0.11322 / 8.00 ( 465) hydrogen bonds : angle 6.36556 / 4.39 ( 1433) Misc. bond : bond 0.41141 / 21.65 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.255 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 107 average time/residue: 0.0704 time to fit residues: 10.5805 Evaluate side-chains 104 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 425 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.0050 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0070 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 overall best weight: 0.4212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 600 ASN ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.166462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.140110 restraints weight = 15466.288| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.17 r_work: 0.3410 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (15 function evaluations) r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.416 8674 Z= 0.128 Angle : 0.586 8.233 11770 Z= 0.297 Chirality : 0.043 0.148 1371 Planarity : 0.004 0.045 1477 Dihedral : 5.756 65.454 1192 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.58 % Allowed : 19.75 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.23 (0.25), residues: 1074 helix: 0.94 (0.23), residues: 505 sheet: 0.21 (0.34), residues: 221 loop : -0.95 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 335 TYR 0.014 0.001 TYR B 479 PHE 0.015 0.001 PHE B 223 TRP 0.028 0.002 TRP A 467 HIS 0.006 0.001 HIS B 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 8673) covalent geometry : angle 0.58577 / 0.30 (11770) hydrogen bonds : bond 0.04501 / 3.06 ( 465) hydrogen bonds : angle 4.79094 / 3.31 ( 1433) Misc. bond : bond 0.41579 / 21.88 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.250 Fit side-chains REVERT: A 370 MET cc_start: 0.8651 (mtt) cc_final: 0.8067 (mmt) REVERT: B 247 ASN cc_start: 0.7601 (m-40) cc_final: 0.7206 (p0) outliers start: 23 outliers final: 15 residues processed: 136 average time/residue: 0.0660 time to fit residues: 13.1564 Evaluate side-chains 119 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 104 optimal weight: 0.2980 chunk 58 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.165643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.139765 restraints weight = 14009.615| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.97 r_work: 0.3405 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (14 function evaluations) r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.500 8674 Z= 0.140 Angle : 0.566 8.090 11770 Z= 0.288 Chirality : 0.043 0.144 1371 Planarity : 0.004 0.040 1477 Dihedral : 5.522 64.236 1187 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.81 % Allowed : 20.20 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.32 (0.25), residues: 1074 helix: 1.10 (0.23), residues: 506 sheet: 0.11 (0.34), residues: 223 loop : -0.93 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 335 TYR 0.012 0.001 TYR B 136 PHE 0.013 0.001 PHE B 75 TRP 0.023 0.002 TRP A 467 HIS 0.003 0.001 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 8673) covalent geometry : angle 0.56585 / 0.29 (11770) hydrogen bonds : bond 0.04453 / 3.00 ( 465) hydrogen bonds : angle 4.62708 / 3.18 ( 1433) Misc. bond : bond 0.49975 / 26.30 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.231 Fit side-chains REVERT: B 247 ASN cc_start: 0.7583 (m-40) cc_final: 0.7170 (p0) outliers start: 25 outliers final: 18 residues processed: 129 average time/residue: 0.0654 time to fit residues: 12.5780 Evaluate side-chains 119 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 69 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 94 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.163076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.134785 restraints weight = 12620.403| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.06 r_work: 0.3375 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (13 function evaluations) r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.761 8674 Z= 0.194 Angle : 0.606 9.059 11770 Z= 0.307 Chirality : 0.044 0.147 1371 Planarity : 0.004 0.040 1477 Dihedral : 5.568 62.657 1187 Min Nonbonded Distance : 1.537 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.25 % Allowed : 20.54 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.22 (0.25), residues: 1074 helix: 0.97 (0.22), residues: 508 sheet: 0.12 (0.34), residues: 222 loop : -0.96 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 335 TYR 0.015 0.002 TYR B 237 PHE 0.015 0.002 PHE B 75 TRP 0.024 0.002 TRP A 467 HIS 0.006 0.001 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.19 ( 8673) covalent geometry : angle 0.60587 / 0.31 (11770) hydrogen bonds : bond 0.04683 / 3.12 ( 465) hydrogen bonds : angle 4.63306 / 3.18 ( 1433) Misc. bond : bond 0.76139 / 40.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.332 Fit side-chains REVERT: A 370 MET cc_start: 0.8737 (mtt) cc_final: 0.8219 (mtt) REVERT: B 9 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8119 (tt) REVERT: B 559 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7070 (mptp) outliers start: 29 outliers final: 21 residues processed: 132 average time/residue: 0.0658 time to fit residues: 12.7547 Evaluate side-chains 130 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 559 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 91 optimal weight: 1.9990 chunk 88 optimal weight: 0.0170 chunk 76 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 16 optimal weight: 0.1980 chunk 38 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 HIS ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.167177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.140125 restraints weight = 10214.143| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.65 r_work: 0.3463 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.446 8674 Z= 0.114 Angle : 0.539 8.046 11770 Z= 0.273 Chirality : 0.041 0.143 1371 Planarity : 0.004 0.039 1477 Dihedral : 5.369 62.319 1187 Min Nonbonded Distance : 1.426 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.70 % Allowed : 20.65 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.25), residues: 1074 helix: 1.30 (0.23), residues: 505 sheet: 0.19 (0.34), residues: 222 loop : -0.92 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 335 TYR 0.012 0.001 TYR B 479 PHE 0.014 0.001 PHE B 223 TRP 0.019 0.002 TRP A 467 HIS 0.003 0.001 HIS B 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 8673) covalent geometry : angle 0.53912 / 0.27 (11770) hydrogen bonds : bond 0.04158 / 2.81 ( 465) hydrogen bonds : angle 4.40816 / 3.02 ( 1433) Misc. bond : bond 0.44599 / 23.47 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 0.206 Fit side-chains REVERT: A 341 MET cc_start: 0.6421 (mtt) cc_final: 0.6069 (mtt) REVERT: A 370 MET cc_start: 0.8675 (mtt) cc_final: 0.8152 (mmt) REVERT: A 436 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8089 (mt) REVERT: B 9 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8097 (tt) REVERT: B 247 ASN cc_start: 0.7573 (m-40) cc_final: 0.7353 (p0) REVERT: B 368 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7233 (mm-30) REVERT: B 551 SER cc_start: 0.8361 (t) cc_final: 0.7986 (m) outliers start: 33 outliers final: 24 residues processed: 134 average time/residue: 0.0603 time to fit residues: 12.0514 Evaluate side-chains 131 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 58 optimal weight: 0.4980 chunk 33 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 0.0170 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.167226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.138650 restraints weight = 12356.930| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.16 r_work: 0.3422 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.421 8674 Z= 0.124 Angle : 0.550 11.741 11770 Z= 0.275 Chirality : 0.042 0.140 1371 Planarity : 0.004 0.040 1477 Dihedral : 5.281 62.153 1187 Min Nonbonded Distance : 1.209 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.26 % Allowed : 20.31 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.65 (0.25), residues: 1074 helix: 1.43 (0.23), residues: 505 sheet: 0.25 (0.34), residues: 223 loop : -0.87 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 335 TYR 0.013 0.001 TYR B 237 PHE 0.013 0.001 PHE B 75 TRP 0.018 0.002 TRP A 467 HIS 0.003 0.001 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 ( 8673) covalent geometry : angle 0.55000 / 0.27 (11770) hydrogen bonds : bond 0.04146 / 2.79 ( 465) hydrogen bonds : angle 4.35338 / 2.98 ( 1433) Misc. bond : bond 0.42142 / 22.18 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 109 time to evaluate : 0.250 Fit side-chains REVERT: A 80 LYS cc_start: 0.8067 (mtpt) cc_final: 0.7854 (ttmt) REVERT: A 341 MET cc_start: 0.6656 (mtt) cc_final: 0.6369 (mtm) REVERT: A 370 MET cc_start: 0.8685 (mtt) cc_final: 0.8139 (mmt) REVERT: A 436 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8044 (mt) REVERT: B 9 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8096 (tt) REVERT: B 247 ASN cc_start: 0.7546 (m-40) cc_final: 0.7291 (p0) REVERT: B 310 MET cc_start: 0.9171 (mmt) cc_final: 0.8296 (mmt) REVERT: B 368 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7176 (mm-30) REVERT: B 505 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7049 (mm-30) REVERT: B 551 SER cc_start: 0.8334 (t) cc_final: 0.7956 (m) outliers start: 38 outliers final: 27 residues processed: 138 average time/residue: 0.0606 time to fit residues: 12.4418 Evaluate side-chains 134 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 467 TRP Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 610 CYS Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 12 optimal weight: 0.9990 chunk 70 optimal weight: 0.0980 chunk 5 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 44 optimal weight: 0.0070 chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 overall best weight: 0.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.167685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.137433 restraints weight = 13693.122| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.08 r_work: 0.3281 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.387 8674 Z= 0.121 Angle : 0.546 9.458 11770 Z= 0.274 Chirality : 0.042 0.140 1371 Planarity : 0.004 0.040 1477 Dihedral : 5.263 62.645 1187 Min Nonbonded Distance : 1.120 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.82 % Allowed : 19.75 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.72 (0.25), residues: 1074 helix: 1.52 (0.23), residues: 504 sheet: 0.27 (0.34), residues: 222 loop : -0.88 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 335 TYR 0.015 0.001 TYR A 372 PHE 0.014 0.001 PHE B 223 TRP 0.018 0.002 TRP A 467 HIS 0.003 0.001 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 8673) covalent geometry : angle 0.54643 / 0.27 (11770) hydrogen bonds : bond 0.04078 / 2.75 ( 465) hydrogen bonds : angle 4.30034 / 2.94 ( 1433) Misc. bond : bond 0.38748 / 20.39 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 0.237 Fit side-chains REVERT: A 341 MET cc_start: 0.6799 (mtt) cc_final: 0.6514 (mtm) REVERT: A 370 MET cc_start: 0.8706 (mtt) cc_final: 0.8109 (mmt) REVERT: A 372 TYR cc_start: 0.7939 (t80) cc_final: 0.7705 (t80) REVERT: A 380 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8225 (tp) REVERT: A 436 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7925 (mt) REVERT: A 608 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8239 (tm-30) REVERT: B 9 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7984 (tt) REVERT: B 247 ASN cc_start: 0.7493 (m-40) cc_final: 0.7206 (p0) REVERT: B 301 ILE cc_start: 0.7299 (OUTLIER) cc_final: 0.6867 (pt) REVERT: B 310 MET cc_start: 0.9184 (mmt) cc_final: 0.8294 (mmt) REVERT: B 368 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7011 (mm-30) REVERT: B 505 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6933 (mm-30) REVERT: B 551 SER cc_start: 0.8178 (t) cc_final: 0.7777 (m) outliers start: 34 outliers final: 28 residues processed: 134 average time/residue: 0.0682 time to fit residues: 13.3674 Evaluate side-chains 135 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 467 TRP Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 53 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 26 optimal weight: 0.0870 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 104 optimal weight: 0.1980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.166648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.139173 restraints weight = 22730.806| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 3.42 r_work: 0.3328 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.332 8674 Z= 0.116 Angle : 0.534 9.229 11770 Z= 0.269 Chirality : 0.041 0.140 1371 Planarity : 0.004 0.040 1477 Dihedral : 5.214 63.770 1187 Min Nonbonded Distance : 1.134 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.37 % Allowed : 21.10 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.83 (0.25), residues: 1074 helix: 1.63 (0.23), residues: 505 sheet: 0.22 (0.34), residues: 227 loop : -0.79 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 335 TYR 0.016 0.001 TYR B 237 PHE 0.013 0.001 PHE B 223 TRP 0.019 0.001 TRP A 467 HIS 0.003 0.001 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.11 ( 8673) covalent geometry : angle 0.53432 / 0.27 (11770) hydrogen bonds : bond 0.03986 / 2.68 ( 465) hydrogen bonds : angle 4.24188 / 2.90 ( 1433) Misc. bond : bond 0.33228 / 17.49 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.314 Fit side-chains REVERT: A 341 MET cc_start: 0.6666 (mtt) cc_final: 0.6438 (mtm) REVERT: A 370 MET cc_start: 0.8635 (mtt) cc_final: 0.8152 (mmt) REVERT: A 380 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8359 (tp) REVERT: A 410 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8199 (mtp-110) REVERT: A 436 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8026 (mp) REVERT: B 9 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8130 (tt) REVERT: B 301 ILE cc_start: 0.7535 (OUTLIER) cc_final: 0.7203 (pt) REVERT: B 310 MET cc_start: 0.9122 (mmt) cc_final: 0.8282 (mmt) REVERT: B 368 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7302 (mm-30) REVERT: B 444 MET cc_start: 0.7702 (tpp) cc_final: 0.7467 (tpp) REVERT: B 505 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7066 (mm-30) REVERT: B 551 SER cc_start: 0.8394 (t) cc_final: 0.8060 (m) outliers start: 30 outliers final: 23 residues processed: 127 average time/residue: 0.0679 time to fit residues: 12.4099 Evaluate side-chains 131 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 410 ARG Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 467 TRP Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 506 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 90 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.166593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.136588 restraints weight = 13624.946| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.05 r_work: 0.3270 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.418 8674 Z= 0.139 Angle : 0.551 9.038 11770 Z= 0.277 Chirality : 0.042 0.140 1371 Planarity : 0.004 0.040 1477 Dihedral : 5.255 63.253 1187 Min Nonbonded Distance : 1.092 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.15 % Allowed : 20.20 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.79 (0.25), residues: 1074 helix: 1.57 (0.23), residues: 506 sheet: 0.20 (0.34), residues: 227 loop : -0.78 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 335 TYR 0.011 0.001 TYR B 136 PHE 0.013 0.001 PHE B 223 TRP 0.019 0.002 TRP A 467 HIS 0.004 0.001 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 8673) covalent geometry : angle 0.55069 / 0.28 (11770) hydrogen bonds : bond 0.04108 / 2.75 ( 465) hydrogen bonds : angle 4.29249 / 2.93 ( 1433) Misc. bond : bond 0.41795 / 22.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 101 time to evaluate : 0.303 Fit side-chains REVERT: A 341 MET cc_start: 0.6926 (mtt) cc_final: 0.6587 (mtm) REVERT: A 370 MET cc_start: 0.8701 (mtt) cc_final: 0.8137 (mmt) REVERT: A 380 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8297 (tp) REVERT: A 410 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8198 (mtp-110) REVERT: A 436 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7872 (mp) REVERT: A 517 CYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8195 (t) REVERT: A 608 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8170 (tm-30) REVERT: B 9 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7951 (tt) REVERT: B 301 ILE cc_start: 0.7319 (OUTLIER) cc_final: 0.6978 (pt) REVERT: B 310 MET cc_start: 0.9191 (mmt) cc_final: 0.8286 (mmt) REVERT: B 368 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7010 (mm-30) REVERT: B 444 MET cc_start: 0.7625 (tpp) cc_final: 0.7323 (tpp) REVERT: B 505 GLU cc_start: 0.7314 (mm-30) cc_final: 0.6959 (mm-30) REVERT: B 551 SER cc_start: 0.8186 (t) cc_final: 0.7781 (m) outliers start: 37 outliers final: 28 residues processed: 132 average time/residue: 0.0630 time to fit residues: 12.0669 Evaluate side-chains 135 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 410 ARG Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 467 TRP Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 517 CYS Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 93 optimal weight: 0.0570 chunk 17 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 80 optimal weight: 0.0980 chunk 58 optimal weight: 0.6980 chunk 48 optimal weight: 0.0040 chunk 46 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 overall best weight: 0.3110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.169374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.141394 restraints weight = 25449.906| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 3.86 r_work: 0.3319 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.262 8674 Z= 0.107 Angle : 0.528 9.142 11770 Z= 0.266 Chirality : 0.041 0.138 1371 Planarity : 0.004 0.040 1477 Dihedral : 5.184 63.841 1187 Min Nonbonded Distance : 1.179 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.70 % Allowed : 21.10 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 (0.25), residues: 1074 helix: 1.74 (0.23), residues: 505 sheet: 0.25 (0.34), residues: 227 loop : -0.77 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 335 TYR 0.011 0.001 TYR B 470 PHE 0.015 0.001 PHE B 223 TRP 0.018 0.001 TRP A 467 HIS 0.002 0.001 HIS B 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 8673) covalent geometry : angle 0.52810 / 0.27 (11770) hydrogen bonds : bond 0.03883 / 2.63 ( 465) hydrogen bonds : angle 4.18779 / 2.86 ( 1433) Misc. bond : bond 0.26205 / 13.79 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 107 time to evaluate : 0.206 Fit side-chains REVERT: A 341 MET cc_start: 0.6898 (mtt) cc_final: 0.6597 (mtm) REVERT: A 410 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8176 (mtp-110) REVERT: B 9 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8118 (tt) REVERT: B 301 ILE cc_start: 0.7505 (OUTLIER) cc_final: 0.7212 (pt) REVERT: B 310 MET cc_start: 0.9115 (mmt) cc_final: 0.8280 (mmt) REVERT: B 368 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7320 (mm-30) REVERT: B 444 MET cc_start: 0.7738 (tpp) cc_final: 0.7513 (tpp) REVERT: B 505 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7086 (mm-30) REVERT: B 551 SER cc_start: 0.8365 (t) cc_final: 0.8056 (m) outliers start: 33 outliers final: 24 residues processed: 132 average time/residue: 0.0659 time to fit residues: 12.6479 Evaluate side-chains 127 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 410 ARG Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 610 CYS Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 100 optimal weight: 3.9990 chunk 74 optimal weight: 0.0030 chunk 15 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 89 optimal weight: 0.0030 chunk 69 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.166277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.139162 restraints weight = 13932.387| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.01 r_work: 0.3444 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.316 8674 Z= 0.125 Angle : 0.562 12.459 11770 Z= 0.277 Chirality : 0.042 0.139 1371 Planarity : 0.004 0.041 1477 Dihedral : 5.211 63.989 1187 Min Nonbonded Distance : 1.114 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.25 % Allowed : 21.55 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.90 (0.25), residues: 1074 helix: 1.69 (0.23), residues: 504 sheet: 0.24 (0.33), residues: 227 loop : -0.76 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 335 TYR 0.010 0.001 TYR B 136 PHE 0.013 0.001 PHE B 223 TRP 0.019 0.002 TRP A 467 HIS 0.004 0.001 HIS A 539 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.12 ( 8673) covalent geometry : angle 0.56172 / 0.28 (11770) hydrogen bonds : bond 0.03998 / 2.69 ( 465) hydrogen bonds : angle 4.23266 / 2.89 ( 1433) Misc. bond : bond 0.31627 / 16.65 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2177.04 seconds wall clock time: 37 minutes 49.74 seconds (2269.74 seconds total)