Starting phenix.real_space_refine on Thu Feb 13 08:15:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hbh_34632/02_2025/8hbh_34632.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hbh_34632/02_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_34632/02_2025/8hbh_34632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hbh_34632/02_2025/8hbh_34632.map" model { file = "/net/cci-nas-00/data/ceres_data/8hbh_34632/02_2025/8hbh_34632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hbh_34632/02_2025/8hbh_34632.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 3, 'HIS:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 5} 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, 'ARG:plan': 1, 'ASP:plan': 5} 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, 'ARG:plan': 1, 'ASP:plan': 5} 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: 7.08, per 1000 atoms: 0.83 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: 2.24 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.05 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: 2.88 Time building geometry restraints manager: 2.56 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: 0.820 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.640 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.040 ------------------------------------------------------------------------------- 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 : 0.008 0.219 8673 Z= 0.515 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.045 0.003 TRP A 467 HIS 0.008 0.001 HIS A 539 PHE 0.021 0.002 PHE A 682 TYR 0.017 0.002 TYR B 237 ARG 0.014 0.001 ARG B 335 *********************** 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 : 0.873 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 107 average time/residue: 0.2207 time to fit residues: 32.6867 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 : 0.926 ------------------------------------------------------------------------------- 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 92 optimal weight: 0.9990 chunk 82 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 33 optimal weight: 0.0980 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.165650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.139141 restraints weight = 25713.596| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 3.82 r_work: 0.3258 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 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 = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8673 Z= 0.201 Angle : 0.589 8.237 11770 Z= 0.300 Chirality : 0.043 0.152 1371 Planarity : 0.004 0.042 1477 Dihedral : 6.820 82.012 1220 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.24 % Allowed : 19.98 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.25), residues: 1074 helix: 0.92 (0.23), residues: 505 sheet: 0.22 (0.34), residues: 221 loop : -0.94 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 467 HIS 0.005 0.001 HIS B 437 PHE 0.014 0.001 PHE B 223 TYR 0.016 0.001 TYR A 372 ARG 0.011 0.001 ARG B 335 *********************** 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 133 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 1.110 Fit side-chains REVERT: A 370 MET cc_start: 0.8660 (mtt) cc_final: 0.8070 (mmt) outliers start: 20 outliers final: 13 residues processed: 129 average time/residue: 0.1978 time to fit residues: 36.7974 Evaluate side-chains 117 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 609 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 105 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 27 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 96 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.165286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.137957 restraints weight = 19863.097| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.73 r_work: 0.3336 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8673 Z= 0.222 Angle : 0.572 8.415 11770 Z= 0.290 Chirality : 0.043 0.142 1371 Planarity : 0.004 0.040 1477 Dihedral : 6.596 77.350 1215 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.03 % Allowed : 20.31 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.25), residues: 1074 helix: 1.08 (0.23), residues: 506 sheet: 0.09 (0.34), residues: 223 loop : -0.91 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 467 HIS 0.004 0.001 HIS B 105 PHE 0.014 0.001 PHE B 223 TYR 0.012 0.001 TYR B 136 ARG 0.006 0.000 ARG B 335 *********************** 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 138 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.989 Fit side-chains REVERT: B 247 ASN cc_start: 0.7535 (m-40) cc_final: 0.7196 (p0) REVERT: B 505 GLU cc_start: 0.7368 (mm-30) cc_final: 0.7088 (mm-30) outliers start: 27 outliers final: 20 residues processed: 134 average time/residue: 0.1813 time to fit residues: 35.6284 Evaluate side-chains 120 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 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 420 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 66 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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** B 608 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.163272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.134588 restraints weight = 18502.388| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.52 r_work: 0.3335 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8673 Z= 0.298 Angle : 0.598 9.156 11770 Z= 0.303 Chirality : 0.044 0.146 1371 Planarity : 0.004 0.041 1477 Dihedral : 6.523 67.735 1215 Min Nonbonded Distance : 1.469 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.82 % Allowed : 20.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.25), residues: 1074 helix: 0.97 (0.22), residues: 508 sheet: 0.07 (0.34), residues: 223 loop : -0.95 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 467 HIS 0.005 0.001 HIS B 105 PHE 0.015 0.002 PHE B 75 TYR 0.015 0.002 TYR B 237 ARG 0.006 0.001 ARG B 335 *********************** 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 141 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 1.004 Fit side-chains REVERT: B 9 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8062 (tt) REVERT: B 505 GLU cc_start: 0.7330 (mm-30) cc_final: 0.7018 (mm-30) REVERT: B 559 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7077 (mptp) outliers start: 34 outliers final: 25 residues processed: 134 average time/residue: 0.1934 time to fit residues: 37.2825 Evaluate side-chains 132 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 559 LYS Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 81 optimal weight: 0.8980 chunk 90 optimal weight: 0.2980 chunk 76 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 0.0770 chunk 13 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS ** 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 = 0.3854 r_free = 0.3854 target = 0.165860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.137281 restraints weight = 25660.767| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 3.90 r_work: 0.3243 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 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 = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8673 Z= 0.200 Angle : 0.551 8.540 11770 Z= 0.278 Chirality : 0.042 0.143 1371 Planarity : 0.004 0.040 1477 Dihedral : 6.270 64.969 1215 Min Nonbonded Distance : 1.260 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.37 % Allowed : 21.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.25), residues: 1074 helix: 1.20 (0.23), residues: 505 sheet: 0.20 (0.34), residues: 220 loop : -0.97 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 467 HIS 0.003 0.001 HIS B 107 PHE 0.014 0.001 PHE B 75 TYR 0.012 0.001 TYR B 136 ARG 0.007 0.000 ARG B 335 *********************** 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 136 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.903 Fit side-chains REVERT: A 341 MET cc_start: 0.6562 (mtt) cc_final: 0.6309 (mtm) REVERT: A 370 MET cc_start: 0.8726 (mtt) cc_final: 0.8188 (mmt) REVERT: A 436 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8173 (mt) REVERT: B 9 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8148 (tt) REVERT: B 247 ASN cc_start: 0.7493 (m-40) cc_final: 0.7234 (p0) REVERT: B 505 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7221 (mm-30) REVERT: B 559 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7046 (mptp) outliers start: 30 outliers final: 24 residues processed: 127 average time/residue: 0.1891 time to fit residues: 34.9037 Evaluate side-chains 131 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 467 TRP Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 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 423 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 496 ILE 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 57 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 88 optimal weight: 0.0670 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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** B 608 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.166932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.136522 restraints weight = 14224.793| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.12 r_work: 0.3265 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 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 = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8673 Z= 0.192 Angle : 0.539 8.274 11770 Z= 0.272 Chirality : 0.042 0.141 1371 Planarity : 0.004 0.039 1477 Dihedral : 6.135 61.956 1215 Min Nonbonded Distance : 1.065 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.15 % Allowed : 20.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.25), residues: 1074 helix: 1.36 (0.23), residues: 504 sheet: 0.27 (0.34), residues: 220 loop : -0.95 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 467 HIS 0.003 0.001 HIS B 107 PHE 0.013 0.001 PHE B 75 TYR 0.014 0.001 TYR B 479 ARG 0.008 0.000 ARG B 335 *********************** 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 149 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 1.095 Fit side-chains REVERT: A 341 MET cc_start: 0.6732 (mtt) cc_final: 0.6446 (mtm) REVERT: A 370 MET cc_start: 0.8699 (mtt) cc_final: 0.8068 (mmt) REVERT: A 436 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7988 (mt) REVERT: B 9 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8004 (tt) REVERT: B 247 ASN cc_start: 0.7406 (m-40) cc_final: 0.7152 (p0) REVERT: B 368 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7028 (mm-30) REVERT: B 505 GLU cc_start: 0.7380 (mm-30) cc_final: 0.7102 (mm-30) REVERT: B 551 SER cc_start: 0.8215 (t) cc_final: 0.7794 (m) REVERT: B 559 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.6920 (mptp) outliers start: 37 outliers final: 29 residues processed: 139 average time/residue: 0.1893 time to fit residues: 38.4514 Evaluate side-chains 136 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 467 TRP Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain 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 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 559 LYS Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 95 optimal weight: 0.0770 chunk 25 optimal weight: 0.0970 chunk 60 optimal weight: 0.4980 chunk 93 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 70 optimal weight: 0.0370 chunk 89 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.3014 ------------------------------------------------------------------------------- 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** B 608 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.169347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.140706 restraints weight = 18287.772| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.13 r_work: 0.3442 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8673 Z= 0.154 Angle : 0.532 12.619 11770 Z= 0.265 Chirality : 0.041 0.139 1371 Planarity : 0.004 0.040 1477 Dihedral : 5.999 63.363 1215 Min Nonbonded Distance : 1.206 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.82 % Allowed : 20.54 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.25), residues: 1074 helix: 1.54 (0.23), residues: 505 sheet: 0.40 (0.34), residues: 220 loop : -0.92 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 467 HIS 0.003 0.001 HIS B 107 PHE 0.014 0.001 PHE B 223 TYR 0.011 0.001 TYR B 470 ARG 0.008 0.000 ARG B 335 *********************** 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 150 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 1.008 Fit side-chains REVERT: A 341 MET cc_start: 0.6710 (mtt) cc_final: 0.6483 (mtm) REVERT: A 370 MET cc_start: 0.8664 (mtt) cc_final: 0.8206 (mmt) REVERT: A 372 TYR cc_start: 0.7772 (t80) cc_final: 0.7559 (t80) REVERT: A 410 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8171 (mtp-110) REVERT: A 436 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7994 (mp) REVERT: B 9 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8148 (tt) REVERT: B 247 ASN cc_start: 0.7546 (m-40) cc_final: 0.7312 (p0) REVERT: B 301 ILE cc_start: 0.7534 (OUTLIER) cc_final: 0.7200 (pt) REVERT: B 310 MET cc_start: 0.9157 (mmt) cc_final: 0.8264 (mmt) REVERT: B 368 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7344 (mm-30) REVERT: B 444 MET cc_start: 0.7675 (tpp) cc_final: 0.7413 (tpp) REVERT: B 505 GLU cc_start: 0.7411 (mm-30) cc_final: 0.7174 (mm-30) REVERT: B 551 SER cc_start: 0.8404 (t) cc_final: 0.8072 (m) outliers start: 34 outliers final: 21 residues processed: 139 average time/residue: 0.2070 time to fit residues: 40.3442 Evaluate side-chains 131 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 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 436 LEU Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 12 LEU 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 473 GLU Chi-restraints excluded: chain B residue 608 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 3 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 66 optimal weight: 0.4980 chunk 99 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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** B 608 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.166303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.136960 restraints weight = 12101.693| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.90 r_work: 0.3276 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8673 Z= 0.236 Angle : 0.574 9.262 11770 Z= 0.286 Chirality : 0.043 0.150 1371 Planarity : 0.004 0.041 1477 Dihedral : 6.088 63.069 1215 Min Nonbonded Distance : 1.060 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.70 % Allowed : 21.10 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.25), residues: 1074 helix: 1.53 (0.23), residues: 507 sheet: 0.26 (0.34), residues: 224 loop : -0.84 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 467 HIS 0.005 0.001 HIS B 105 PHE 0.013 0.001 PHE B 75 TYR 0.015 0.001 TYR A 372 ARG 0.008 0.000 ARG A 349 *********************** 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 : 0.994 Fit side-chains REVERT: A 341 MET cc_start: 0.6785 (mtt) cc_final: 0.6519 (mtm) REVERT: A 370 MET cc_start: 0.8688 (mtt) cc_final: 0.8120 (mmt) REVERT: A 436 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7855 (mp) REVERT: A 517 CYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8171 (t) REVERT: B 9 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8006 (tt) REVERT: B 247 ASN cc_start: 0.7390 (m-40) cc_final: 0.7171 (p0) REVERT: B 301 ILE cc_start: 0.7312 (OUTLIER) cc_final: 0.6959 (pt) REVERT: B 310 MET cc_start: 0.9174 (mmt) cc_final: 0.8269 (mmt) REVERT: B 368 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7019 (mm-30) REVERT: B 444 MET cc_start: 0.7567 (tpp) cc_final: 0.7259 (tpp) REVERT: B 505 GLU cc_start: 0.7259 (mm-30) cc_final: 0.6992 (mm-30) REVERT: B 551 SER cc_start: 0.8173 (t) cc_final: 0.7763 (m) REVERT: B 559 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.6913 (mptp) outliers start: 33 outliers final: 25 residues processed: 131 average time/residue: 0.1937 time to fit residues: 35.9671 Evaluate side-chains 137 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU 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 436 LEU Chi-restraints excluded: chain A residue 467 TRP Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 517 CYS Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 559 LYS Chi-restraints excluded: chain B residue 608 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 91 optimal weight: 2.9990 chunk 23 optimal weight: 0.0000 chunk 41 optimal weight: 0.0060 chunk 106 optimal weight: 0.0970 chunk 43 optimal weight: 0.4980 chunk 75 optimal weight: 0.0980 chunk 59 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 74 optimal weight: 0.4980 chunk 46 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 overall best weight: 0.1398 ------------------------------------------------------------------------------- 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 = 0.3896 r_free = 0.3896 target = 0.169856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.141861 restraints weight = 11981.037| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.79 r_work: 0.3477 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8673 Z= 0.145 Angle : 0.545 9.759 11770 Z= 0.271 Chirality : 0.041 0.139 1371 Planarity : 0.004 0.040 1477 Dihedral : 5.970 64.058 1215 Min Nonbonded Distance : 1.185 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.59 % Allowed : 21.55 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1074 helix: 1.70 (0.23), residues: 504 sheet: 0.29 (0.34), residues: 225 loop : -0.78 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 467 HIS 0.002 0.000 HIS B 107 PHE 0.015 0.001 PHE B 223 TYR 0.024 0.001 TYR A 372 ARG 0.008 0.000 ARG B 335 *********************** 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 144 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 1.027 Fit side-chains REVERT: A 341 MET cc_start: 0.6607 (mtt) cc_final: 0.6359 (mtm) REVERT: A 410 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8138 (mtp-110) REVERT: A 436 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7945 (mp) REVERT: B 9 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8100 (tt) REVERT: B 301 ILE cc_start: 0.7495 (OUTLIER) cc_final: 0.7188 (pt) REVERT: B 310 MET cc_start: 0.9121 (mmt) cc_final: 0.8309 (mmt) REVERT: B 368 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7290 (mm-30) REVERT: B 444 MET cc_start: 0.7639 (tpp) cc_final: 0.7420 (tpp) REVERT: B 505 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7133 (mm-30) REVERT: B 551 SER cc_start: 0.8329 (t) cc_final: 0.8004 (m) outliers start: 32 outliers final: 24 residues processed: 134 average time/residue: 0.2083 time to fit residues: 39.2405 Evaluate side-chains 133 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 309 MET 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 436 LEU Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 99 optimal weight: 0.0470 chunk 22 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 14 optimal weight: 8.9990 chunk 55 optimal weight: 0.2980 chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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** B 608 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.168317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.140623 restraints weight = 18363.906| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.11 r_work: 0.3397 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8673 Z= 0.182 Angle : 0.549 9.466 11770 Z= 0.274 Chirality : 0.042 0.141 1371 Planarity : 0.004 0.041 1477 Dihedral : 5.969 64.242 1215 Min Nonbonded Distance : 1.119 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.48 % Allowed : 21.66 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.25), residues: 1074 helix: 1.72 (0.23), residues: 504 sheet: 0.34 (0.34), residues: 224 loop : -0.80 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 467 HIS 0.004 0.001 HIS A 539 PHE 0.013 0.001 PHE B 223 TYR 0.013 0.001 TYR B 237 ARG 0.008 0.000 ARG B 335 ********************** 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 137 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 0.984 Fit side-chains REVERT: A 341 MET cc_start: 0.6599 (mtt) cc_final: 0.6390 (mtm) REVERT: A 410 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8127 (mtp-110) REVERT: A 436 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7949 (mp) REVERT: B 9 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8113 (tt) REVERT: B 301 ILE cc_start: 0.7601 (OUTLIER) cc_final: 0.7315 (pt) REVERT: B 310 MET cc_start: 0.9027 (mmt) cc_final: 0.8179 (mmt) REVERT: B 551 SER cc_start: 0.8339 (t) cc_final: 0.8015 (m) outliers start: 31 outliers final: 24 residues processed: 128 average time/residue: 0.1971 time to fit residues: 35.9173 Evaluate side-chains 131 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU 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 309 MET 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 436 LEU Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 320 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 506 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 44 optimal weight: 0.0020 chunk 95 optimal weight: 0.0970 chunk 50 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 overall best weight: 0.4586 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.166700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.138623 restraints weight = 12098.145| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.79 r_work: 0.3460 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8673 Z= 0.176 Angle : 0.548 9.355 11770 Z= 0.274 Chirality : 0.042 0.140 1371 Planarity : 0.004 0.040 1477 Dihedral : 5.938 64.329 1215 Min Nonbonded Distance : 1.129 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.25 % Allowed : 22.11 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.25), residues: 1074 helix: 1.75 (0.23), residues: 505 sheet: 0.36 (0.34), residues: 224 loop : -0.78 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 467 HIS 0.003 0.001 HIS A 539 PHE 0.014 0.001 PHE B 223 TYR 0.014 0.001 TYR B 479 ARG 0.008 0.000 ARG B 335 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5058.30 seconds wall clock time: 90 minutes 10.54 seconds (5410.54 seconds total)