Starting phenix.real_space_refine on Thu Mar 13 09:56:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hbe_34623/03_2025/8hbe_34623.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hbe_34623/03_2025/8hbe_34623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hbe_34623/03_2025/8hbe_34623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hbe_34623/03_2025/8hbe_34623.map" model { file = "/net/cci-nas-00/data/ceres_data/8hbe_34623/03_2025/8hbe_34623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hbe_34623/03_2025/8hbe_34623.cif" } resolution = 3.2 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= 0.003 sd= 0.185 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: 5 Type Number sf(0) Gaussians Fe 1 7.16 5 S 60 5.16 5 C 5534 2.51 5 N 1457 2.21 5 O 1558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8610 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4120 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 542, 4117 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 515} Chain breaks: 5 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 7, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 14, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 125 Conformer: "B" Number of residues, atoms: 542, 4117 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 515} Chain breaks: 5 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 7, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 14, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 125 bond proxies already assigned to first conformer: 4196 Chain: "B" Number of atoms: 4447 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 572, 4443 Classifications: {'peptide': 572} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 548} Chain breaks: 2 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 104 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ARG:plan': 4, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 81 Conformer: "B" Number of residues, atoms: 572, 4443 Classifications: {'peptide': 572} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 548} Chain breaks: 2 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 104 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ARG:plan': 4, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 81 bond proxies already assigned to first conformer: 4529 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.25, per 1000 atoms: 1.07 Number of scatterers: 8610 At special positions: 0 Unit cell: (75.24, 95.095, 149.435, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 1 26.01 S 60 16.00 O 1558 8.00 N 1457 7.00 C 5534 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: 2.40 Conformation dependent library (CDL) restraints added in 2.1 seconds 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 9 sheets defined 49.8% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 70 through 83 Processing helix chain 'A' and resid 85 through 101 Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 128 through 148 removed outlier: 3.580A pdb=" N ASP A 148 " --> pdb=" O CYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 174 removed outlier: 4.900A pdb=" N SER A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 228 removed outlier: 3.712A pdb=" N TYR A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 242 removed outlier: 4.039A pdb=" N HIS A 241 " --> pdb=" O PRO A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 286 Processing helix chain 'A' and resid 302 through 310 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 392 through 397 removed outlier: 3.561A pdb=" N ARG A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 403 Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.398A pdb=" N ALA A 408 " --> pdb=" O ILE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 421 removed outlier: 4.533A pdb=" N GLY A 416 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU A 417 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 425 removed outlier: 4.240A pdb=" N LEU A 425 " --> pdb=" O GLN A 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 422 through 425' Processing helix chain 'A' and resid 426 through 458 removed outlier: 3.965A pdb=" N GLY A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 457 " --> pdb=" O LEU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 469 Processing helix chain 'A' and resid 489 through 496 Processing helix chain 'A' and resid 498 through 521 Processing helix chain 'A' and resid 544 through 563 Processing helix chain 'A' and resid 598 through 610 removed outlier: 3.759A pdb=" N THR A 602 " --> pdb=" O GLY A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 628 removed outlier: 4.711A pdb=" N ASP A 628 " --> pdb=" O ARG A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 642 Processing helix chain 'B' and resid 2 through 29 removed outlier: 3.566A pdb=" N ASN B 6 " --> pdb=" O TYR B 2 " (cutoff:3.500A) Proline residue: B 19 - end of helix removed outlier: 3.923A pdb=" N TRP B 22 " --> pdb=" O GLY B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.802A pdb=" N THR B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 81 Processing helix chain 'B' and resid 83 through 90 Processing helix chain 'B' and resid 93 through 109 removed outlier: 4.679A pdb=" N ASP B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ALA B 103 " --> pdb=" O GLN B 99 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 157 removed outlier: 3.862A pdb=" N VAL B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 330 through 335 removed outlier: 3.739A pdb=" N THR B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 355 removed outlier: 4.098A pdb=" N ASP B 351 " --> pdb=" O ASP B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 395 removed outlier: 3.740A pdb=" N THR B 366 " --> pdb=" O GLU B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 408 removed outlier: 3.841A pdb=" N HIS B 408 " --> pdb=" O ASN B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 436 Processing helix chain 'B' and resid 439 through 461 Processing helix chain 'B' and resid 491 through 507 Processing helix chain 'B' and resid 544 through 557 removed outlier: 3.966A pdb=" N ASN B 548 " --> pdb=" O GLY B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 573 Processing sheet with id=AA1, first strand: chain 'A' and resid 189 through 193 removed outlier: 4.060A pdb=" N SER A 189 " --> pdb=" O PHE A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 289 through 292 removed outlier: 6.650A pdb=" N VAL A 347 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 523 through 525 removed outlier: 4.515A pdb=" N CYS A 533 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LYS A 476 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ALA A 584 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N SER A 478 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 6.027A 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 525 removed outlier: 4.515A pdb=" N CYS A 533 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LYS A 476 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ALA A 584 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N SER A 478 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL A 582 " --> pdb=" O SER A 478 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ILE A 616 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 119 through 124 removed outlier: 6.563A pdb=" N GLN B 178 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU B 182 " --> pdb=" O ASP B 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.691A pdb=" N VAL B 229 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASP B 224 " --> pdb=" O VAL B 229 " (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 470 through 472 removed outlier: 4.469A pdb=" N MET B 480 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ARG B 416 " --> pdb=" O THR B 530 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N THR B 530 " --> pdb=" O ARG B 416 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASP B 418 " --> pdb=" O VAL B 528 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL B 528 " --> pdb=" O ASP B 418 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 529 " --> pdb=" O PHE B 543 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 470 through 472 removed outlier: 4.469A pdb=" N MET B 480 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ARG B 416 " --> pdb=" O THR B 530 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N THR B 530 " --> pdb=" O ARG B 416 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASP B 418 " --> pdb=" O VAL B 528 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL B 528 " --> pdb=" O ASP B 418 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ASN B 563 " --> pdb=" O ILE B 519 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE B 521 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE B 562 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET B 599 " --> pdb=" O VAL B 590 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL B 601 " --> pdb=" O GLY B 588 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY B 588 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N PHE B 603 " --> pdb=" O HIS B 586 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N HIS B 586 " --> pdb=" O PHE B 603 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N SER B 605 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N LEU B 584 " --> pdb=" O SER B 605 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 511 through 512 519 hydrogen bonds defined for protein. 1475 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: 3.00 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 3489 1.38 - 1.56: 5206 1.56 - 1.74: 0 1.74 - 1.92: 93 1.92 - 2.10: 3 Bond restraints: 8791 Sorted by residual: bond pdb=" CA PHE B 359 " pdb=" C PHE B 359 " ideal model delta sigma weight residual 1.526 1.471 0.055 1.28e-02 6.10e+03 1.82e+01 bond pdb=" C3B HEM B1000 " pdb=" CAB HEM B1000 " ideal model delta sigma weight residual 1.544 1.468 0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" CA ASN B 329 " pdb=" C ASN B 329 " ideal model delta sigma weight residual 1.523 1.475 0.048 1.31e-02 5.83e+03 1.36e+01 bond pdb=" CA ARG B 360 " pdb=" C ARG B 360 " ideal model delta sigma weight residual 1.523 1.473 0.050 1.42e-02 4.96e+03 1.23e+01 bond pdb=" C3C HEM B1000 " pdb=" CAC HEM B1000 " ideal model delta sigma weight residual 1.544 1.475 0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 8786 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 11842 3.33 - 6.67: 86 6.67 - 10.00: 6 10.00 - 13.34: 0 13.34 - 16.67: 2 Bond angle restraints: 11936 Sorted by residual: angle pdb=" N PHE B 359 " pdb=" CA PHE B 359 " pdb=" C PHE B 359 " ideal model delta sigma weight residual 112.26 104.89 7.37 1.32e+00 5.74e-01 3.12e+01 angle pdb=" N ALA B 438 " pdb=" CA ALA B 438 " pdb=" C ALA B 438 " ideal model delta sigma weight residual 111.55 117.05 -5.50 1.37e+00 5.33e-01 1.61e+01 angle pdb=" C PRO A 613 " pdb=" N ARG A 614 " pdb=" CA ARG A 614 " ideal model delta sigma weight residual 121.54 128.61 -7.07 1.91e+00 2.74e-01 1.37e+01 angle pdb=" N LYS A 317 " pdb=" CA LYS A 317 " pdb=" C LYS A 317 " ideal model delta sigma weight residual 111.00 119.53 -8.53 2.80e+00 1.28e-01 9.29e+00 angle pdb=" C3D HEM B1000 " pdb=" CAD HEM B1000 " pdb=" CBD HEM B1000 " ideal model delta sigma weight residual 109.50 118.26 -8.76 3.00e+00 1.11e-01 8.52e+00 ... (remaining 11931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 4633 16.65 - 33.30: 464 33.30 - 49.95: 136 49.95 - 66.60: 18 66.60 - 83.25: 15 Dihedral angle restraints: 5266 sinusoidal: 2022 harmonic: 3244 Sorted by residual: dihedral pdb=" C2B HEM B1000 " pdb=" C3B HEM B1000 " pdb=" CAB HEM B1000 " pdb=" CBB HEM B1000 " ideal model delta sinusoidal sigma weight residual 0.00 71.48 -71.48 2 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" CA PHE A 301 " pdb=" C PHE A 301 " pdb=" N GLY A 302 " pdb=" CA GLY A 302 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA GLY B 35 " pdb=" C GLY B 35 " pdb=" N GLN B 36 " pdb=" CA GLN B 36 " ideal model delta harmonic sigma weight residual -180.00 -161.27 -18.73 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 5263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 973 0.044 - 0.087: 298 0.087 - 0.131: 95 0.131 - 0.174: 14 0.174 - 0.218: 6 Chirality restraints: 1386 Sorted by residual: chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA MET B 328 " pdb=" N MET B 328 " pdb=" C MET B 328 " pdb=" CB MET B 328 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA MET B 444 " pdb=" N MET B 444 " pdb=" C MET B 444 " pdb=" CB MET B 444 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1383 not shown) Planarity restraints: 1516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 466 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO B 467 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 467 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 467 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 442 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.98e+00 pdb=" C GLY B 442 " -0.034 2.00e-02 2.50e+03 pdb=" O GLY B 442 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA B 443 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 258 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO B 259 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 259 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 259 " 0.024 5.00e-02 4.00e+02 ... (remaining 1513 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1280 2.75 - 3.29: 7984 3.29 - 3.83: 14192 3.83 - 4.36: 16730 4.36 - 4.90: 29797 Nonbonded interactions: 69983 Sorted by model distance: nonbonded pdb=" OE1 GLU B 473 " pdb=" NH1 ARG B 539 " model vdw 2.217 3.120 nonbonded pdb=" O LEU B 251 " pdb=" NZ LYS B 281 " model vdw 2.251 3.120 nonbonded pdb=" OH TYR A 510 " pdb=" O GLY A 529 " model vdw 2.264 3.040 nonbonded pdb=" OG1 THR A 168 " pdb=" O ASN A 343 " model vdw 2.308 3.040 nonbonded pdb=" NH1 ARG B 121 " pdb=" OH TYR B 136 " model vdw 2.318 3.120 ... (remaining 69978 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.770 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 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 : 0.007 0.211 8791 Z= 0.422 Angle : 0.734 16.674 11936 Z= 0.366 Chirality : 0.048 0.218 1386 Planarity : 0.005 0.050 1516 Dihedral : 15.140 83.252 3166 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.20 (0.25), residues: 1097 helix: 0.45 (0.23), residues: 523 sheet: -0.14 (0.32), residues: 247 loop : -0.85 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 602 HIS 0.013 0.001 HIS A 224 PHE 0.017 0.002 PHE B 603 TYR 0.013 0.002 TYR B 135 ARG 0.005 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.901 Fit side-chains REVERT: B 355 LEU cc_start: 0.6425 (mp) cc_final: 0.6218 (mp) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2132 time to fit residues: 31.7682 Evaluate side-chains 103 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9980 chunk 84 optimal weight: 0.0020 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS A 468 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.165319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.117294 restraints weight = 16509.484| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.60 r_work: 0.2990 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.0654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8791 Z= 0.227 Angle : 0.591 13.344 11936 Z= 0.292 Chirality : 0.043 0.163 1386 Planarity : 0.004 0.040 1516 Dihedral : 5.883 86.538 1200 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.20 % Allowed : 11.98 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.13 (0.25), residues: 1097 helix: 0.77 (0.22), residues: 523 sheet: -0.11 (0.32), residues: 241 loop : -0.66 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 467 HIS 0.009 0.001 HIS A 224 PHE 0.016 0.001 PHE A 141 TYR 0.015 0.001 TYR B 49 ARG 0.003 0.000 ARG B 539 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: B 404 ASN cc_start: 0.7099 (t0) cc_final: 0.6840 (t0) REVERT: B 599 MET cc_start: 0.6855 (OUTLIER) cc_final: 0.6347 (ptt) outliers start: 11 outliers final: 7 residues processed: 117 average time/residue: 0.1877 time to fit residues: 31.8718 Evaluate side-chains 111 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 599 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 46 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 0.0070 chunk 90 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS A 468 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.162417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.127307 restraints weight = 24177.776| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 6.21 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.0692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8791 Z= 0.368 Angle : 0.650 13.830 11936 Z= 0.319 Chirality : 0.045 0.164 1386 Planarity : 0.004 0.042 1516 Dihedral : 5.957 86.725 1200 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.85 % Allowed : 13.62 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.05 (0.25), residues: 1097 helix: 0.71 (0.22), residues: 522 sheet: -0.18 (0.31), residues: 245 loop : -0.69 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 602 HIS 0.009 0.001 HIS A 224 PHE 0.016 0.002 PHE A 141 TYR 0.017 0.002 TYR B 49 ARG 0.005 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7322 (mp) REVERT: B 599 MET cc_start: 0.7243 (ptp) cc_final: 0.6802 (ptt) outliers start: 17 outliers final: 11 residues processed: 120 average time/residue: 0.1905 time to fit residues: 33.0839 Evaluate side-chains 116 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 423 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 110 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 66 optimal weight: 0.0770 chunk 30 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 GLN A 548 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.166024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.114401 restraints weight = 18053.679| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 3.35 r_work: 0.2912 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8791 Z= 0.206 Angle : 0.566 12.962 11936 Z= 0.277 Chirality : 0.042 0.148 1386 Planarity : 0.004 0.040 1516 Dihedral : 5.672 82.602 1200 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.74 % Allowed : 14.05 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.33 (0.25), residues: 1097 helix: 1.00 (0.23), residues: 522 sheet: -0.16 (0.31), residues: 245 loop : -0.54 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 602 HIS 0.008 0.001 HIS A 224 PHE 0.015 0.001 PHE A 141 TYR 0.018 0.001 TYR B 49 ARG 0.003 0.000 ARG B 539 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.6807 (OUTLIER) cc_final: 0.6447 (mp) REVERT: A 344 MET cc_start: 0.8614 (mmm) cc_final: 0.8385 (mmt) REVERT: B 384 GLU cc_start: 0.8021 (tp30) cc_final: 0.7253 (tt0) REVERT: B 599 MET cc_start: 0.6774 (ptp) cc_final: 0.6236 (ptt) outliers start: 16 outliers final: 10 residues processed: 119 average time/residue: 0.1856 time to fit residues: 32.1076 Evaluate side-chains 116 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 423 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 109 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 1 optimal weight: 0.1980 chunk 20 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 0 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS A 468 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.166576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.114400 restraints weight = 16802.277| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.16 r_work: 0.2961 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8791 Z= 0.198 Angle : 0.558 12.468 11936 Z= 0.273 Chirality : 0.042 0.142 1386 Planarity : 0.004 0.040 1516 Dihedral : 5.557 82.995 1200 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.63 % Allowed : 15.03 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.53 (0.25), residues: 1097 helix: 1.16 (0.23), residues: 522 sheet: -0.06 (0.31), residues: 244 loop : -0.46 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 602 HIS 0.007 0.001 HIS A 224 PHE 0.015 0.001 PHE A 141 TYR 0.019 0.001 TYR B 49 ARG 0.003 0.000 ARG A 593 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.6849 (OUTLIER) cc_final: 0.6474 (mp) REVERT: B 454 TYR cc_start: 0.7795 (m-10) cc_final: 0.7552 (m-10) REVERT: B 599 MET cc_start: 0.6709 (ptp) cc_final: 0.6158 (ptt) outliers start: 15 outliers final: 13 residues processed: 123 average time/residue: 0.1927 time to fit residues: 34.2418 Evaluate side-chains 118 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 572 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 18 optimal weight: 0.0970 chunk 26 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 86 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 HIS A 468 GLN ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.168085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.125709 restraints weight = 11304.137| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.09 r_work: 0.3091 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8791 Z= 0.177 Angle : 0.543 12.029 11936 Z= 0.266 Chirality : 0.041 0.141 1386 Planarity : 0.004 0.039 1516 Dihedral : 5.460 82.066 1200 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.96 % Allowed : 14.71 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 1097 helix: 1.30 (0.23), residues: 522 sheet: -0.15 (0.31), residues: 249 loop : -0.31 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 602 HIS 0.003 0.001 HIS B 408 PHE 0.014 0.001 PHE A 141 TYR 0.012 0.001 TYR A 145 ARG 0.004 0.000 ARG B 539 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.6676 (OUTLIER) cc_final: 0.6315 (mp) REVERT: B 328 MET cc_start: 0.8000 (ptp) cc_final: 0.7762 (mtt) REVERT: B 384 GLU cc_start: 0.7896 (tp30) cc_final: 0.7076 (tt0) REVERT: B 454 TYR cc_start: 0.7569 (m-10) cc_final: 0.7341 (m-10) REVERT: B 473 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7690 (pt0) REVERT: B 599 MET cc_start: 0.6543 (ptp) cc_final: 0.6024 (ptt) outliers start: 18 outliers final: 13 residues processed: 126 average time/residue: 0.2076 time to fit residues: 36.9438 Evaluate side-chains 125 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 572 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 97 optimal weight: 0.2980 chunk 102 optimal weight: 0.2980 chunk 24 optimal weight: 0.2980 chunk 85 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 5 optimal weight: 10.0000 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 GLN ** B 134 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 = 0.3768 r_free = 0.3768 target = 0.168344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.118812 restraints weight = 14383.227| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.49 r_work: 0.3056 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8791 Z= 0.166 Angle : 0.534 11.817 11936 Z= 0.261 Chirality : 0.041 0.136 1386 Planarity : 0.004 0.048 1516 Dihedral : 5.383 81.947 1200 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.63 % Allowed : 15.58 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.80 (0.26), residues: 1097 helix: 1.42 (0.23), residues: 522 sheet: -0.12 (0.31), residues: 249 loop : -0.22 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 602 HIS 0.003 0.001 HIS B 408 PHE 0.014 0.001 PHE A 141 TYR 0.011 0.001 TYR B 237 ARG 0.003 0.000 ARG B 539 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.6724 (OUTLIER) cc_final: 0.6377 (mp) REVERT: B 454 TYR cc_start: 0.7684 (m-10) cc_final: 0.7479 (m-10) REVERT: B 473 GLU cc_start: 0.7624 (pt0) cc_final: 0.7416 (mm-30) REVERT: B 599 MET cc_start: 0.6629 (ptp) cc_final: 0.6077 (ptt) outliers start: 15 outliers final: 12 residues processed: 126 average time/residue: 0.1988 time to fit residues: 35.7568 Evaluate side-chains 119 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 572 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 44 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS A 468 GLN ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.166585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.112775 restraints weight = 21936.718| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.86 r_work: 0.2911 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8791 Z= 0.223 Angle : 0.559 12.444 11936 Z= 0.273 Chirality : 0.042 0.138 1386 Planarity : 0.004 0.039 1516 Dihedral : 5.459 83.101 1200 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.18 % Allowed : 15.69 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.72 (0.26), residues: 1097 helix: 1.33 (0.23), residues: 521 sheet: -0.10 (0.31), residues: 249 loop : -0.26 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 602 HIS 0.010 0.001 HIS A 224 PHE 0.014 0.001 PHE A 162 TYR 0.011 0.001 TYR B 135 ARG 0.004 0.000 ARG A 593 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.6914 (OUTLIER) cc_final: 0.6538 (mp) REVERT: A 344 MET cc_start: 0.8505 (mmm) cc_final: 0.8297 (mmt) REVERT: B 384 GLU cc_start: 0.8027 (tp30) cc_final: 0.7231 (tt0) REVERT: B 454 TYR cc_start: 0.7771 (m-10) cc_final: 0.7486 (m-10) REVERT: B 599 MET cc_start: 0.6584 (ptp) cc_final: 0.6067 (ptt) outliers start: 20 outliers final: 16 residues processed: 125 average time/residue: 0.1948 time to fit residues: 34.7951 Evaluate side-chains 126 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain B residue 2 TYR Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 572 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 75 optimal weight: 0.2980 chunk 96 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS A 468 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.164882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.114152 restraints weight = 16572.398| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.78 r_work: 0.2985 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8791 Z= 0.251 Angle : 0.579 12.838 11936 Z= 0.283 Chirality : 0.043 0.141 1386 Planarity : 0.004 0.039 1516 Dihedral : 5.541 83.318 1200 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.96 % Allowed : 16.12 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.64 (0.25), residues: 1097 helix: 1.25 (0.23), residues: 520 sheet: -0.11 (0.31), residues: 249 loop : -0.29 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 602 HIS 0.011 0.001 HIS A 224 PHE 0.013 0.002 PHE A 141 TYR 0.012 0.001 TYR B 135 ARG 0.005 0.000 ARG A 593 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.6759 (OUTLIER) cc_final: 0.6406 (mp) REVERT: A 344 MET cc_start: 0.8555 (mmm) cc_final: 0.8277 (mmt) REVERT: B 527 GLU cc_start: 0.6991 (pp20) cc_final: 0.6576 (pt0) REVERT: B 599 MET cc_start: 0.6623 (ptp) cc_final: 0.6093 (ptt) outliers start: 18 outliers final: 17 residues processed: 120 average time/residue: 0.2019 time to fit residues: 34.4186 Evaluate side-chains 122 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain B residue 2 TYR Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 572 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 64 optimal weight: 0.0470 chunk 89 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 chunk 7 optimal weight: 0.0470 chunk 28 optimal weight: 0.1980 chunk 91 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 12 optimal weight: 0.0970 overall best weight: 0.2174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS A 468 GLN ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.168923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.133214 restraints weight = 21693.172| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 5.62 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3404 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3404 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8791 Z= 0.151 Angle : 0.543 11.559 11936 Z= 0.266 Chirality : 0.041 0.137 1386 Planarity : 0.004 0.038 1516 Dihedral : 5.378 80.518 1200 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.74 % Allowed : 16.78 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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 (0.26), residues: 1097 helix: 1.51 (0.23), residues: 522 sheet: -0.12 (0.31), residues: 249 loop : -0.11 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 602 HIS 0.017 0.001 HIS A 224 PHE 0.016 0.001 PHE A 141 TYR 0.011 0.001 TYR B 237 ARG 0.004 0.000 ARG A 593 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.7179 (mp) REVERT: B 527 GLU cc_start: 0.6845 (pp20) cc_final: 0.6487 (pt0) REVERT: B 599 MET cc_start: 0.6871 (ptp) cc_final: 0.6409 (ptt) outliers start: 16 outliers final: 13 residues processed: 117 average time/residue: 0.1951 time to fit residues: 33.1750 Evaluate side-chains 121 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain B residue 2 TYR Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 572 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 100 optimal weight: 0.8980 chunk 107 optimal weight: 0.0370 chunk 38 optimal weight: 1.9990 chunk 74 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 chunk 60 optimal weight: 0.0060 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 0.0570 chunk 39 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS B 134 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.170879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.120305 restraints weight = 16904.949| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.16 r_work: 0.3024 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 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 : 0.002 0.029 8791 Z= 0.145 Angle : 0.524 10.505 11936 Z= 0.257 Chirality : 0.040 0.138 1386 Planarity : 0.004 0.039 1516 Dihedral : 5.211 81.158 1200 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.96 % Allowed : 16.67 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 1.17 (0.26), residues: 1097 helix: 1.72 (0.23), residues: 514 sheet: -0.04 (0.31), residues: 249 loop : 0.10 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 602 HIS 0.003 0.001 HIS A 224 PHE 0.015 0.001 PHE A 162 TYR 0.011 0.001 TYR B 237 ARG 0.004 0.000 ARG A 593 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4966.31 seconds wall clock time: 86 minutes 3.76 seconds (5163.76 seconds total)