Starting phenix.real_space_refine on Sat Aug 23 00:43:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hbh_34632/08_2025/8hbh_34632.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hbh_34632/08_2025/8hbh_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hbh_34632/08_2025/8hbh_34632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hbh_34632/08_2025/8hbh_34632.map" model { file = "/net/cci-nas-00/data/ceres_data/8hbh_34632/08_2025/8hbh_34632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hbh_34632/08_2025/8hbh_34632.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.158 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-2.0-5787/lib/python3.9/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: 3.27, per 1000 atoms: 0.38 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: 0.87 Conformation dependent library (CDL) restraints added in 402.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.33 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: 1.69 Time building geometry restraints manager: 1.08 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 - 17.76: 4582 17.76 - 35.53: 497 35.53 - 53.29: 104 53.29 - 71.06: 21 71.06 - 88.82: 4 Dihedral angle restraints: 5208 sinusoidal: 2014 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 5205 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: 0.000 Normalize map: mean=0, sd=1: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.040 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 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 : 15.288 88.820 3138 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 aren 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 covalent geometry : bond 0.00755 ( 8673) covalent geometry : angle 0.83959 (11770) hydrogen bonds : bond 0.11322 ( 465) hydrogen bonds : angle 6.36556 ( 1433) Misc. bond : bond 0.41141 ( 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 : 0.248 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 107 average time/residue: 0.1054 time to fit residues: 15.6075 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 : 0.355 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3858 r_free = 0.3858 target = 0.165913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.139719 restraints weight = 15471.729| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.17 r_work: 0.3407 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 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 = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.0817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.414 8674 Z= 0.129 Angle : 0.589 8.200 11770 Z= 0.300 Chirality : 0.043 0.151 1371 Planarity : 0.004 0.042 1477 Dihedral : 6.825 82.007 1220 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.47 % Allowed : 19.87 % 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 aren 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 : -0.94 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 335 TYR 0.016 0.001 TYR A 372 PHE 0.014 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 covalent geometry : bond 0.00292 ( 8673) covalent geometry : angle 0.58898 (11770) hydrogen bonds : bond 0.04581 ( 465) hydrogen bonds : angle 4.83093 ( 1433) Misc. bond : bond 0.41434 ( 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 135 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.257 Fit side-chains REVERT: A 370 MET cc_start: 0.8653 (mtt) cc_final: 0.8059 (mmt) outliers start: 22 outliers final: 14 residues processed: 131 average time/residue: 0.0858 time to fit residues: 16.2299 Evaluate side-chains 119 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 58 optimal weight: 0.3980 chunk 81 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 41 optimal weight: 0.2980 chunk 71 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3857 r_free = 0.3857 target = 0.165823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.139356 restraints weight = 13991.661| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.02 r_work: 0.3421 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.472 8674 Z= 0.135 Angle : 0.566 8.150 11770 Z= 0.287 Chirality : 0.042 0.144 1371 Planarity : 0.004 0.045 1477 Dihedral : 6.616 79.108 1215 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.69 % Allowed : 20.54 % Favored : 76.77 % 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 aren not related in a simple way. whole: 0.34 (0.25), residues: 1074 helix: 1.11 (0.23), residues: 506 sheet: 0.11 (0.34), residues: 223 loop : -0.91 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 335 TYR 0.012 0.001 TYR B 136 PHE 0.014 0.001 PHE B 223 TRP 0.023 0.002 TRP A 467 HIS 0.003 0.001 HIS B 437 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8673) covalent geometry : angle 0.56574 (11770) hydrogen bonds : bond 0.04455 ( 465) hydrogen bonds : angle 4.64915 ( 1433) Misc. bond : bond 0.47189 ( 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 135 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.318 Fit side-chains REVERT: B 247 ASN cc_start: 0.7647 (m-40) cc_final: 0.7230 (p0) REVERT: B 505 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7120 (mm-30) outliers start: 24 outliers final: 20 residues processed: 130 average time/residue: 0.0617 time to fit residues: 12.2710 Evaluate side-chains 122 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 48 optimal weight: 0.0770 chunk 106 optimal weight: 8.9990 chunk 94 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3843 r_free = 0.3843 target = 0.164641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.136598 restraints weight = 12605.910| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.94 r_work: 0.3404 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.598 8674 Z= 0.156 Angle : 0.572 8.791 11770 Z= 0.290 Chirality : 0.043 0.144 1371 Planarity : 0.004 0.048 1477 Dihedral : 6.452 71.377 1215 Min Nonbonded Distance : 1.691 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.25 % Allowed : 20.43 % Favored : 76.32 % 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 aren not related in a simple way. whole: 0.34 (0.25), residues: 1074 helix: 1.12 (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 0.009 0.000 ARG B 335 TYR 0.015 0.001 TYR B 237 PHE 0.014 0.001 PHE B 75 TRP 0.022 0.002 TRP A 467 HIS 0.004 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 8673) covalent geometry : angle 0.57175 (11770) hydrogen bonds : bond 0.04460 ( 465) hydrogen bonds : angle 4.54923 ( 1433) Misc. bond : bond 0.59837 ( 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 134 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.297 Fit side-chains REVERT: A 370 MET cc_start: 0.8697 (mtt) cc_final: 0.8090 (mtt) REVERT: B 9 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8162 (tt) REVERT: B 247 ASN cc_start: 0.7539 (m-40) cc_final: 0.7197 (p0) REVERT: B 368 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7309 (mm-30) REVERT: B 505 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7133 (mm-30) REVERT: B 559 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7019 (mptp) outliers start: 29 outliers final: 21 residues processed: 128 average time/residue: 0.0800 time to fit residues: 15.0672 Evaluate side-chains 123 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 402 ASP 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 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: 2.9990 chunk 88 optimal weight: 0.3980 chunk 76 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.166024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.138917 restraints weight = 10230.577| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.64 r_work: 0.3448 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 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 = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.509 8674 Z= 0.131 Angle : 0.548 8.553 11770 Z= 0.277 Chirality : 0.042 0.142 1371 Planarity : 0.004 0.049 1477 Dihedral : 6.266 66.045 1215 Min Nonbonded Distance : 1.439 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.15 % Allowed : 19.87 % Favored : 75.98 % 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 aren not related in a simple way. whole: 0.46 (0.25), residues: 1074 helix: 1.26 (0.23), residues: 506 sheet: 0.14 (0.34), residues: 223 loop : -0.92 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 335 TYR 0.012 0.001 TYR B 470 PHE 0.014 0.001 PHE B 223 TRP 0.020 0.002 TRP A 467 HIS 0.003 0.001 HIS A 539 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8673) covalent geometry : angle 0.54843 (11770) hydrogen bonds : bond 0.04257 ( 465) hydrogen bonds : angle 4.42771 ( 1433) Misc. bond : bond 0.50868 ( 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 144 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 107 time to evaluate : 0.365 Fit side-chains REVERT: A 341 MET cc_start: 0.6466 (mtt) cc_final: 0.6123 (mtt) REVERT: A 370 MET cc_start: 0.8698 (mtt) cc_final: 0.8040 (mmt) REVERT: B 9 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8124 (tt) REVERT: B 368 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7211 (mm-30) REVERT: B 505 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7155 (mm-30) REVERT: B 559 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7035 (mptp) outliers start: 37 outliers final: 28 residues processed: 135 average time/residue: 0.0849 time to fit residues: 16.6947 Evaluate side-chains 134 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 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 334 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 ASP 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 104 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 473 GLU Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 559 LYS 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: 0.4980 chunk 14 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.167392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.140399 restraints weight = 12372.855| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.91 r_work: 0.3430 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 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 = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.427 8674 Z= 0.121 Angle : 0.544 11.081 11770 Z= 0.272 Chirality : 0.042 0.141 1371 Planarity : 0.004 0.052 1477 Dihedral : 6.140 63.256 1215 Min Nonbonded Distance : 1.211 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.70 % Allowed : 20.31 % Favored : 75.98 % 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 aren not related in a simple way. whole: 0.62 (0.25), residues: 1074 helix: 1.40 (0.23), residues: 505 sheet: 0.26 (0.34), residues: 222 loop : -0.89 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 335 TYR 0.013 0.001 TYR B 237 PHE 0.014 0.001 PHE B 223 TRP 0.019 0.002 TRP A 467 HIS 0.003 0.001 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8673) covalent geometry : angle 0.54416 (11770) hydrogen bonds : bond 0.04136 ( 465) hydrogen bonds : angle 4.35391 ( 1433) Misc. bond : bond 0.42737 ( 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 146 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 0.374 Fit side-chains REVERT: A 341 MET cc_start: 0.6606 (mtt) cc_final: 0.6336 (mtm) REVERT: A 370 MET cc_start: 0.8678 (mtt) cc_final: 0.8047 (mmt) REVERT: A 380 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8389 (tp) REVERT: B 9 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8132 (tt) REVERT: B 368 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7238 (mm-30) REVERT: B 505 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7189 (mm-30) REVERT: B 551 SER cc_start: 0.8399 (t) cc_final: 0.8032 (m) outliers start: 33 outliers final: 22 residues processed: 137 average time/residue: 0.0760 time to fit residues: 15.4219 Evaluate side-chains 128 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 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 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 104 LEU Chi-restraints excluded: chain B residue 256 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 12 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.165937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.138131 restraints weight = 13740.343| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.06 r_work: 0.3406 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 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 = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.506 8674 Z= 0.145 Angle : 0.564 8.979 11770 Z= 0.282 Chirality : 0.043 0.143 1371 Planarity : 0.004 0.053 1477 Dihedral : 6.171 61.844 1215 Min Nonbonded Distance : 1.070 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.70 % Allowed : 20.31 % Favored : 75.98 % 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 aren not related in a simple way. whole: 0.63 (0.25), residues: 1074 helix: 1.43 (0.23), residues: 504 sheet: 0.23 (0.34), residues: 222 loop : -0.89 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 335 TYR 0.013 0.001 TYR A 372 PHE 0.014 0.001 PHE B 223 TRP 0.020 0.002 TRP A 467 HIS 0.004 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 8673) covalent geometry : angle 0.56435 (11770) hydrogen bonds : bond 0.04231 ( 465) hydrogen bonds : angle 4.36319 ( 1433) Misc. bond : bond 0.50582 ( 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 140 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 107 time to evaluate : 0.348 Fit side-chains REVERT: A 341 MET cc_start: 0.6706 (mtt) cc_final: 0.6491 (mtm) REVERT: A 370 MET cc_start: 0.8698 (mtt) cc_final: 0.8064 (mtt) REVERT: B 9 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8170 (tt) REVERT: B 310 MET cc_start: 0.9150 (mmt) cc_final: 0.8279 (mmt) REVERT: B 368 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7301 (mm-30) REVERT: B 505 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7248 (mm-30) REVERT: B 559 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7040 (mptp) outliers start: 33 outliers final: 29 residues processed: 132 average time/residue: 0.0793 time to fit residues: 15.0285 Evaluate side-chains 135 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE 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 423 ASP 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 104 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 559 LYS 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: 0.8980 chunk 45 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 26 optimal weight: 0.2980 chunk 83 optimal weight: 0.0770 chunk 46 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.166862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.139474 restraints weight = 22856.399| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 3.46 r_work: 0.3337 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.419 8674 Z= 0.122 Angle : 0.547 8.928 11770 Z= 0.274 Chirality : 0.042 0.141 1371 Planarity : 0.004 0.057 1477 Dihedral : 6.082 62.412 1215 Min Nonbonded Distance : 1.130 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.70 % Allowed : 20.54 % Favored : 75.76 % 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 aren not related in a simple way. whole: 0.73 (0.25), residues: 1074 helix: 1.52 (0.23), residues: 504 sheet: 0.18 (0.34), residues: 227 loop : -0.79 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 335 TYR 0.013 0.001 TYR B 237 PHE 0.014 0.001 PHE B 223 TRP 0.020 0.002 TRP A 467 HIS 0.003 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8673) covalent geometry : angle 0.54694 (11770) hydrogen bonds : bond 0.04069 ( 465) hydrogen bonds : angle 4.30078 ( 1433) Misc. bond : bond 0.41909 ( 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 139 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.344 Fit side-chains REVERT: A 341 MET cc_start: 0.6778 (mtt) cc_final: 0.6477 (mtm) REVERT: A 370 MET cc_start: 0.8653 (mtt) cc_final: 0.8092 (mmt) REVERT: A 380 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8366 (tp) REVERT: A 410 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8233 (mtp-110) REVERT: B 9 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8116 (tt) REVERT: B 60 ASN cc_start: 0.8617 (m-40) cc_final: 0.8414 (m-40) REVERT: B 310 MET cc_start: 0.9123 (mmt) cc_final: 0.8246 (mmt) REVERT: B 368 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7210 (mm-30) REVERT: B 505 GLU cc_start: 0.7275 (mm-30) cc_final: 0.7074 (mm-30) REVERT: B 551 SER cc_start: 0.8359 (t) cc_final: 0.8003 (m) REVERT: B 559 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7041 (mptp) outliers start: 33 outliers final: 27 residues processed: 132 average time/residue: 0.0818 time to fit residues: 15.5302 Evaluate side-chains 133 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 104 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 559 LYS Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 90 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 105 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 101 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.165593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.137863 restraints weight = 13628.209| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.12 r_work: 0.3409 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.472 8674 Z= 0.140 Angle : 0.561 8.654 11770 Z= 0.282 Chirality : 0.042 0.140 1371 Planarity : 0.004 0.057 1477 Dihedral : 6.094 62.527 1215 Min Nonbonded Distance : 1.080 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.70 % Allowed : 20.88 % 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 aren not related in a simple way. whole: 0.71 (0.25), residues: 1074 helix: 1.50 (0.23), residues: 505 sheet: 0.16 (0.34), residues: 227 loop : -0.79 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 335 TYR 0.011 0.001 TYR B 136 PHE 0.014 0.001 PHE B 223 TRP 0.020 0.002 TRP A 467 HIS 0.004 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8673) covalent geometry : angle 0.56065 (11770) hydrogen bonds : bond 0.04165 ( 465) hydrogen bonds : angle 4.31766 ( 1433) Misc. bond : bond 0.47248 ( 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 137 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 0.264 Fit side-chains REVERT: A 341 MET cc_start: 0.6865 (mtt) cc_final: 0.6559 (mtm) REVERT: A 370 MET cc_start: 0.8701 (mtt) cc_final: 0.8141 (mmt) REVERT: A 380 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8503 (tp) REVERT: A 410 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8316 (mtp-110) REVERT: B 9 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8131 (tt) REVERT: B 310 MET cc_start: 0.9154 (mmt) cc_final: 0.8314 (mmt) REVERT: B 368 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7290 (mm-30) REVERT: B 559 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7030 (mptp) outliers start: 33 outliers final: 26 residues processed: 130 average time/residue: 0.0784 time to fit residues: 14.4888 Evaluate side-chains 131 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU 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 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 104 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 256 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 506 ILE Chi-restraints excluded: chain B residue 559 LYS 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: 1.9990 chunk 17 optimal weight: 0.1980 chunk 85 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 58 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 95 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.165428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.136853 restraints weight = 25608.302| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 3.90 r_work: 0.3264 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.389 8674 Z= 0.123 Angle : 0.553 8.787 11770 Z= 0.277 Chirality : 0.042 0.139 1371 Planarity : 0.004 0.060 1477 Dihedral : 6.021 62.738 1215 Min Nonbonded Distance : 1.136 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.37 % Allowed : 21.44 % 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 aren not related in a simple way. whole: 0.81 (0.25), residues: 1074 helix: 1.60 (0.23), residues: 504 sheet: 0.23 (0.34), residues: 227 loop : -0.78 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 335 TYR 0.013 0.001 TYR B 237 PHE 0.014 0.001 PHE B 223 TRP 0.020 0.002 TRP A 467 HIS 0.003 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8673) covalent geometry : angle 0.55300 (11770) hydrogen bonds : bond 0.04020 ( 465) hydrogen bonds : angle 4.25879 ( 1433) Misc. bond : bond 0.38860 ( 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 132 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.267 Fit side-chains REVERT: A 341 MET cc_start: 0.6867 (mtt) cc_final: 0.6564 (mtm) REVERT: A 370 MET cc_start: 0.8651 (mtt) cc_final: 0.8156 (mmt) REVERT: A 410 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8282 (mtp-110) REVERT: B 9 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8146 (tt) REVERT: B 310 MET cc_start: 0.9153 (mmt) cc_final: 0.8335 (mmt) REVERT: B 368 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7336 (mm-30) REVERT: B 444 MET cc_start: 0.7741 (tpp) cc_final: 0.7481 (tpp) REVERT: B 551 SER cc_start: 0.8418 (t) cc_final: 0.8077 (m) REVERT: B 559 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7014 (mptp) outliers start: 30 outliers final: 26 residues processed: 125 average time/residue: 0.0817 time to fit residues: 14.6375 Evaluate side-chains 130 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU 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 423 ASP 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 104 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 256 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 506 ILE Chi-restraints excluded: chain B residue 559 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 100 optimal weight: 0.7980 chunk 74 optimal weight: 0.0970 chunk 15 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 89 optimal weight: 0.0370 chunk 69 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.167409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.139761 restraints weight = 13902.230| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.14 r_work: 0.3430 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.349 8674 Z= 0.120 Angle : 0.562 12.072 11770 Z= 0.279 Chirality : 0.042 0.138 1371 Planarity : 0.004 0.060 1477 Dihedral : 6.011 63.383 1215 Min Nonbonded Distance : 1.120 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.03 % Allowed : 22.00 % Favored : 74.97 % 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 aren not related in a simple way. whole: 0.87 (0.25), residues: 1074 helix: 1.65 (0.23), residues: 504 sheet: 0.24 (0.34), residues: 227 loop : -0.74 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 335 TYR 0.011 0.001 TYR B 136 PHE 0.013 0.001 PHE B 223 TRP 0.020 0.002 TRP A 467 HIS 0.003 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8673) covalent geometry : angle 0.56240 (11770) hydrogen bonds : bond 0.04015 ( 465) hydrogen bonds : angle 4.25673 ( 1433) Misc. bond : bond 0.34891 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2611.61 seconds wall clock time: 45 minutes 17.52 seconds (2717.52 seconds total)