Starting phenix.real_space_refine on Tue Sep 24 20:52:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbh_34632/09_2024/8hbh_34632.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbh_34632/09_2024/8hbh_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbh_34632/09_2024/8hbh_34632.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbh_34632/09_2024/8hbh_34632.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbh_34632/09_2024/8hbh_34632.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbh_34632/09_2024/8hbh_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 7.17, per 1000 atoms: 0.84 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: 2.22 Conformation dependent library (CDL) restraints added in 1.5 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: 1.00 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: 2.59 Time building geometry restraints manager: 2.55 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: 0.700 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.630 Find NCS groups from input model: 0.130 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.580 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 0.937 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 107 average time/residue: 0.2127 time to fit residues: 31.4149 Evaluate side-chains 104 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 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 fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 0.918 Fit side-chains REVERT: A 370 MET cc_start: 0.8437 (mtt) cc_final: 0.7869 (mmt) outliers start: 20 outliers final: 13 residues processed: 129 average time/residue: 0.1835 time to fit residues: 34.0366 Evaluate side-chains 117 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 55 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 82 optimal weight: 0.3980 chunk 67 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 88 optimal weight: 0.0570 chunk 98 optimal weight: 0.7980 chunk 33 optimal weight: 0.3980 chunk 79 optimal weight: 0.6980 overall best weight: 0.4298 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8673 Z= 0.181 Angle : 0.551 8.026 11770 Z= 0.280 Chirality : 0.042 0.141 1371 Planarity : 0.004 0.039 1477 Dihedral : 6.536 78.965 1215 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.92 % Allowed : 20.43 % 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: 0.39 (0.25), residues: 1074 helix: 1.17 (0.23), residues: 506 sheet: 0.13 (0.34), residues: 223 loop : -0.90 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 467 HIS 0.004 0.001 HIS B 437 PHE 0.014 0.001 PHE B 223 TYR 0.012 0.001 TYR B 479 ARG 0.008 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 fitting. rotamer outliers: 26 poor density : 112 time to evaluate : 0.943 Fit side-chains REVERT: B 247 ASN cc_start: 0.7369 (m-40) cc_final: 0.6812 (p0) REVERT: B 368 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6633 (mm-30) REVERT: B 505 GLU cc_start: 0.6905 (mm-30) cc_final: 0.6550 (mm-30) outliers start: 26 outliers final: 18 residues processed: 132 average time/residue: 0.1749 time to fit residues: 33.5846 Evaluate side-chains 122 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1165 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 : 0.558 8.592 11770 Z= 0.283 Chirality : 0.042 0.145 1371 Planarity : 0.004 0.040 1477 Dihedral : 6.386 71.449 1215 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % 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: 0.42 (0.25), residues: 1074 helix: 1.19 (0.23), residues: 506 sheet: 0.15 (0.34), residues: 223 loop : -0.92 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 467 HIS 0.004 0.001 HIS B 105 PHE 0.014 0.001 PHE B 223 TYR 0.014 0.001 TYR B 237 ARG 0.007 0.000 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 133 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 106 time to evaluate : 0.970 Fit side-chains REVERT: B 9 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7476 (tt) REVERT: B 247 ASN cc_start: 0.7310 (m-40) cc_final: 0.6812 (p0) REVERT: B 368 GLU cc_start: 0.7360 (mt-10) cc_final: 0.6623 (mm-30) REVERT: B 505 GLU cc_start: 0.6943 (mm-30) cc_final: 0.6575 (mm-30) REVERT: B 559 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.6555 (mptp) outliers start: 27 outliers final: 21 residues processed: 128 average time/residue: 0.1841 time to fit residues: 34.0756 Evaluate side-chains 126 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 103 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 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 9 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 559 LYS 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 59 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 0.0040 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1272 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= 0.208 Angle : 0.544 8.489 11770 Z= 0.276 Chirality : 0.042 0.143 1371 Planarity : 0.004 0.040 1477 Dihedral : 6.235 65.499 1215 Min Nonbonded Distance : 1.453 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.04 % Allowed : 19.87 % Favored : 76.09 % 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: 0.51 (0.25), residues: 1074 helix: 1.30 (0.23), residues: 506 sheet: 0.16 (0.34), residues: 223 loop : -0.88 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 467 HIS 0.003 0.001 HIS B 105 PHE 0.013 0.001 PHE B 223 TYR 0.011 0.001 TYR B 470 ARG 0.008 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 140 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 104 time to evaluate : 0.973 Fit side-chains REVERT: A 370 MET cc_start: 0.8525 (mtt) cc_final: 0.7827 (mtt) REVERT: B 9 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7461 (tt) REVERT: B 247 ASN cc_start: 0.7303 (m-40) cc_final: 0.6908 (p0) REVERT: B 368 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6589 (mm-30) REVERT: B 505 GLU cc_start: 0.6934 (mm-30) cc_final: 0.6603 (mm-30) outliers start: 36 outliers final: 29 residues processed: 131 average time/residue: 0.1758 time to fit residues: 33.5663 Evaluate side-chains 132 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 102 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 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 104 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 473 GLU Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1359 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= 0.212 Angle : 0.552 11.069 11770 Z= 0.277 Chirality : 0.042 0.143 1371 Planarity : 0.004 0.040 1477 Dihedral : 6.180 62.513 1215 Min Nonbonded Distance : 1.171 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.83 % Allowed : 19.87 % Favored : 75.31 % 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: 0.58 (0.25), residues: 1074 helix: 1.34 (0.23), residues: 509 sheet: 0.21 (0.34), residues: 222 loop : -0.86 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 467 HIS 0.004 0.001 HIS B 105 PHE 0.013 0.001 PHE B 223 TYR 0.013 0.001 TYR B 237 ARG 0.007 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 152 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 109 time to evaluate : 0.972 Fit side-chains REVERT: A 80 LYS cc_start: 0.8051 (mtpt) cc_final: 0.7831 (ttmt) REVERT: A 370 MET cc_start: 0.8532 (mtt) cc_final: 0.7852 (mtt) REVERT: B 9 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7471 (tt) REVERT: B 247 ASN cc_start: 0.7274 (m-40) cc_final: 0.6921 (p0) REVERT: B 310 MET cc_start: 0.9254 (mmt) cc_final: 0.8288 (mmt) REVERT: B 368 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6534 (mm-30) REVERT: B 505 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6556 (mm-30) REVERT: B 559 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.6543 (mptp) outliers start: 43 outliers final: 34 residues processed: 140 average time/residue: 0.1785 time to fit residues: 36.1604 Evaluate side-chains 135 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 99 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 467 TRP Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 610 CYS Chi-restraints excluded: chain 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 104 LEU 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 473 GLU Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 559 LYS Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 88 optimal weight: 0.0980 chunk 58 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8673 Z= 0.189 Angle : 0.546 9.190 11770 Z= 0.273 Chirality : 0.042 0.141 1371 Planarity : 0.004 0.040 1477 Dihedral : 6.132 62.263 1215 Min Nonbonded Distance : 1.109 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.04 % Allowed : 20.09 % Favored : 75.87 % 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: 0.66 (0.25), residues: 1074 helix: 1.46 (0.23), residues: 504 sheet: 0.22 (0.34), residues: 222 loop : -0.88 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 467 HIS 0.003 0.001 HIS B 107 PHE 0.013 0.001 PHE B 223 TYR 0.013 0.001 TYR A 372 ARG 0.007 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 143 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 107 time to evaluate : 1.585 Fit side-chains REVERT: A 370 MET cc_start: 0.8545 (mtt) cc_final: 0.8004 (mmt) REVERT: B 9 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7450 (tt) REVERT: B 247 ASN cc_start: 0.7296 (m-40) cc_final: 0.6950 (p0) REVERT: B 301 ILE cc_start: 0.6790 (OUTLIER) cc_final: 0.6106 (pt) REVERT: B 310 MET cc_start: 0.9252 (mmt) cc_final: 0.8305 (mmt) REVERT: B 335 ARG cc_start: 0.7848 (mtm110) cc_final: 0.7629 (mtm110) REVERT: B 368 GLU cc_start: 0.7307 (mt-10) cc_final: 0.6534 (mm-30) REVERT: B 505 GLU cc_start: 0.6866 (mm-30) cc_final: 0.6554 (mm-30) REVERT: B 551 SER cc_start: 0.7577 (t) cc_final: 0.7054 (m) REVERT: B 559 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.6538 (mptp) outliers start: 36 outliers final: 29 residues processed: 133 average time/residue: 0.1852 time to fit residues: 35.6828 Evaluate side-chains 135 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 103 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 467 TRP Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 610 CYS Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 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 506 ILE Chi-restraints excluded: chain B residue 559 LYS 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 62 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.0060 chunk 66 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8673 Z= 0.201 Angle : 0.559 8.939 11770 Z= 0.279 Chirality : 0.042 0.142 1371 Planarity : 0.004 0.040 1477 Dihedral : 6.129 62.553 1215 Min Nonbonded Distance : 1.109 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.93 % Allowed : 20.20 % Favored : 75.87 % 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: 0.71 (0.25), residues: 1074 helix: 1.50 (0.23), residues: 505 sheet: 0.19 (0.34), residues: 226 loop : -0.82 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 467 HIS 0.003 0.001 HIS B 105 PHE 0.013 0.001 PHE B 75 TYR 0.028 0.001 TYR A 372 ARG 0.007 0.000 ARG B 335 *********************** 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 fitting. rotamer outliers: 35 poor density : 104 time to evaluate : 0.938 Fit side-chains REVERT: A 370 MET cc_start: 0.8532 (mtt) cc_final: 0.8002 (mmt) REVERT: B 9 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7463 (tt) REVERT: B 247 ASN cc_start: 0.7289 (m-40) cc_final: 0.6954 (p0) REVERT: B 301 ILE cc_start: 0.6781 (OUTLIER) cc_final: 0.6143 (pt) REVERT: B 310 MET cc_start: 0.9255 (mmt) cc_final: 0.8300 (mmt) REVERT: B 335 ARG cc_start: 0.7845 (mtm110) cc_final: 0.7622 (mtm110) REVERT: B 368 GLU cc_start: 0.7288 (mt-10) cc_final: 0.6523 (mm-30) REVERT: B 505 GLU cc_start: 0.6865 (mm-30) cc_final: 0.6579 (mm-30) REVERT: B 551 SER cc_start: 0.7570 (t) cc_final: 0.7054 (m) REVERT: B 559 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.6535 (mptp) outliers start: 35 outliers final: 28 residues processed: 130 average time/residue: 0.1889 time to fit residues: 34.6800 Evaluate side-chains 133 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 102 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 363 VAL 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 467 TRP Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 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 97 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 0.3980 chunk 30 optimal weight: 0.9990 chunk 88 optimal weight: 0.0870 chunk 92 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8673 Z= 0.190 Angle : 0.553 8.846 11770 Z= 0.276 Chirality : 0.042 0.140 1371 Planarity : 0.004 0.040 1477 Dihedral : 6.081 62.969 1215 Min Nonbonded Distance : 1.119 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 4.38 % Allowed : 19.87 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.56 (0.23), residues: 504 sheet: 0.21 (0.34), residues: 226 loop : -0.80 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 467 HIS 0.003 0.001 HIS B 105 PHE 0.014 0.001 PHE B 223 TYR 0.011 0.001 TYR B 136 ARG 0.007 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 fitting. rotamer outliers: 39 poor density : 105 time to evaluate : 0.963 Fit side-chains REVERT: A 410 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8342 (mtp-110) REVERT: B 9 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7450 (tt) REVERT: B 247 ASN cc_start: 0.7285 (m-40) cc_final: 0.6940 (p0) REVERT: B 301 ILE cc_start: 0.6807 (OUTLIER) cc_final: 0.6449 (pt) REVERT: B 310 MET cc_start: 0.9214 (mmt) cc_final: 0.8277 (mmt) REVERT: B 368 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6537 (mm-30) REVERT: B 444 MET cc_start: 0.6722 (tpp) cc_final: 0.6389 (tpp) REVERT: B 505 GLU cc_start: 0.6777 (mm-30) cc_final: 0.6458 (mm-30) REVERT: B 551 SER cc_start: 0.7562 (t) cc_final: 0.7050 (m) REVERT: B 559 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.6532 (mptp) outliers start: 39 outliers final: 32 residues processed: 134 average time/residue: 0.1922 time to fit residues: 36.6585 Evaluate side-chains 135 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 99 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 410 ARG Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 467 TRP Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain 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 104 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 559 LYS Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.1980 chunk 71 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 99 optimal weight: 0.0870 chunk 86 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 0.0270 chunk 68 optimal weight: 0.4980 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.3016 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1851 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= 0.155 Angle : 0.535 8.869 11770 Z= 0.268 Chirality : 0.041 0.137 1371 Planarity : 0.004 0.039 1477 Dihedral : 5.937 64.520 1215 Min Nonbonded Distance : 1.181 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.14 % Allowed : 21.10 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.92 (0.25), residues: 1074 helix: 1.71 (0.23), residues: 508 sheet: 0.28 (0.34), residues: 226 loop : -0.79 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 467 HIS 0.002 0.001 HIS B 107 PHE 0.013 0.001 PHE B 223 TYR 0.013 0.001 TYR B 237 ARG 0.009 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 134 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 106 time to evaluate : 0.957 Fit side-chains REVERT: A 410 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8224 (mtp-110) REVERT: B 247 ASN cc_start: 0.7279 (m-40) cc_final: 0.6905 (p0) REVERT: B 301 ILE cc_start: 0.6798 (OUTLIER) cc_final: 0.6539 (pt) REVERT: B 307 LYS cc_start: 0.8485 (tttt) cc_final: 0.8264 (ttpt) REVERT: B 444 MET cc_start: 0.6728 (tpp) cc_final: 0.6399 (tpp) REVERT: B 505 GLU cc_start: 0.6799 (mm-30) cc_final: 0.6486 (mm-30) REVERT: B 551 SER cc_start: 0.7516 (t) cc_final: 0.7041 (m) outliers start: 28 outliers final: 22 residues processed: 125 average time/residue: 0.1880 time to fit residues: 33.5839 Evaluate side-chains 126 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 102 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 410 ARG Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain 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 420 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 496 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 88 optimal weight: 0.2980 chunk 10 optimal weight: 0.0980 chunk 15 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.168695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.140288 restraints weight = 18241.766| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.45 r_work: 0.3408 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8673 Z= 0.182 Angle : 0.560 12.937 11770 Z= 0.277 Chirality : 0.042 0.149 1371 Planarity : 0.004 0.040 1477 Dihedral : 5.952 64.629 1215 Min Nonbonded Distance : 1.115 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.92 % Allowed : 21.89 % 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: 0.94 (0.25), residues: 1074 helix: 1.70 (0.23), residues: 509 sheet: 0.31 (0.34), residues: 226 loop : -0.75 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 467 HIS 0.003 0.001 HIS B 105 PHE 0.014 0.001 PHE B 223 TYR 0.010 0.001 TYR B 136 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: 2047.18 seconds wall clock time: 37 minutes 9.86 seconds (2229.86 seconds total)