Starting phenix.real_space_refine on Tue Apr 29 16:57:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hbe_34623/04_2025/8hbe_34623.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hbe_34623/04_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_34623/04_2025/8hbe_34623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hbe_34623/04_2025/8hbe_34623.map" model { file = "/net/cci-nas-00/data/ceres_data/8hbe_34623/04_2025/8hbe_34623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hbe_34623/04_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-5669/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: 9.74, per 1000 atoms: 1.13 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: 2.42 Conformation dependent library (CDL) restraints added in 2.2 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: 1.06 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: 3.05 Time building geometry restraints manager: 2.87 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: 1.040 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: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 30.660 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.420 ------------------------------------------------------------------------------- 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 : 0.008 0.414 8792 Z= 0.294 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 Details of bonding type rmsd hydrogen bonds : bond 0.11333 ( 485) hydrogen bonds : angle 6.01594 ( 1475) covalent geometry : bond 0.00677 ( 8791) covalent geometry : angle 0.73416 (11936) Misc. bond : bond 0.41360 ( 1) *********************** 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 : 0.871 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: 0.2066 time to fit residues: 30.3883 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 : 0.987 ------------------------------------------------------------------------------- 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: 0.7980 chunk 100 optimal weight: 0.9980 overall best weight: 0.7388 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.166282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.118359 restraints weight = 16460.934| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 3.15 r_work: 0.2941 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.0589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.238 8792 Z= 0.148 Angle : 0.598 13.993 11936 Z= 0.296 Chirality : 0.043 0.161 1386 Planarity : 0.004 0.040 1516 Dihedral : 5.937 87.524 1200 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.98 % Allowed : 12.20 % 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: 0.11 (0.25), residues: 1097 helix: 0.76 (0.22), residues: 523 sheet: -0.12 (0.32), residues: 241 loop : -0.68 (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 0.014 0.001 TYR B 49 ARG 0.003 0.000 ARG B 139 Details of bonding type rmsd hydrogen bonds : bond 0.04081 ( 485) hydrogen bonds : angle 4.79555 ( 1475) covalent geometry : bond 0.00357 ( 8791) covalent geometry : angle 0.59832 (11936) Misc. bond : bond 0.23837 ( 1) *********************** 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 120 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: B 404 ASN cc_start: 0.7074 (t0) cc_final: 0.6818 (t0) REVERT: B 599 MET cc_start: 0.6853 (ptp) cc_final: 0.6344 (ptt) outliers start: 9 outliers final: 7 residues processed: 116 average time/residue: 0.1816 time to fit residues: 30.5655 Evaluate side-chains 109 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 224 HIS 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 46 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 10 optimal weight: 0.0770 chunk 90 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 4 optimal weight: 20.0000 chunk 105 optimal weight: 1.9990 overall best weight: 0.7344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.165716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.130863 restraints weight = 24143.054| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 6.15 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3363 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3363 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.223 8792 Z= 0.140 Angle : 0.577 12.815 11936 Z= 0.283 Chirality : 0.042 0.154 1386 Planarity : 0.004 0.040 1516 Dihedral : 5.769 85.499 1200 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.74 % Allowed : 13.18 % Favored : 85.08 % 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: 0.30 (0.25), residues: 1097 helix: 0.94 (0.22), residues: 523 sheet: -0.14 (0.31), residues: 245 loop : -0.53 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 467 HIS 0.015 0.001 HIS A 224 PHE 0.017 0.001 PHE A 141 TYR 0.018 0.001 TYR B 49 ARG 0.004 0.000 ARG B 539 Details of bonding type rmsd hydrogen bonds : bond 0.03803 ( 485) hydrogen bonds : angle 4.57008 ( 1475) covalent geometry : bond 0.00339 ( 8791) covalent geometry : angle 0.57678 (11936) Misc. bond : bond 0.22329 ( 1) *********************** 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 126 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7359 (mp) REVERT: B 404 ASN cc_start: 0.7597 (t0) cc_final: 0.7365 (t0) REVERT: B 599 MET cc_start: 0.7157 (ptp) cc_final: 0.6725 (ptt) outliers start: 16 outliers final: 12 residues processed: 120 average time/residue: 0.1792 time to fit residues: 31.2358 Evaluate side-chains 116 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 218 ILE 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 Chi-restraints excluded: chain B residue 475 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 110 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.164597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.111657 restraints weight = 18074.288| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.03 r_work: 0.2931 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.227 8792 Z= 0.169 Angle : 0.591 13.351 11936 Z= 0.289 Chirality : 0.043 0.150 1386 Planarity : 0.004 0.040 1516 Dihedral : 5.741 85.045 1200 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.74 % Allowed : 13.62 % Favored : 84.64 % 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: 0.32 (0.25), residues: 1097 helix: 0.97 (0.22), residues: 521 sheet: -0.13 (0.31), residues: 245 loop : -0.56 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 602 HIS 0.003 0.001 HIS A 578 PHE 0.015 0.002 PHE A 141 TYR 0.018 0.001 TYR B 49 ARG 0.003 0.000 ARG B 539 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 485) hydrogen bonds : angle 4.49118 ( 1475) covalent geometry : bond 0.00418 ( 8791) covalent geometry : angle 0.59132 (11936) Misc. bond : bond 0.22707 ( 1) *********************** 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 123 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.6858 (OUTLIER) cc_final: 0.6462 (mp) REVERT: B 404 ASN cc_start: 0.7049 (t0) cc_final: 0.6843 (t0) REVERT: B 539 ARG cc_start: 0.7772 (ptm160) cc_final: 0.7549 (ptm160) REVERT: B 599 MET cc_start: 0.6767 (ptp) cc_final: 0.6196 (ptt) outliers start: 16 outliers final: 10 residues processed: 118 average time/residue: 0.1772 time to fit residues: 30.4030 Evaluate side-chains 118 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 218 ILE 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: 2.9990 chunk 76 optimal weight: 0.8980 chunk 83 optimal weight: 0.4980 chunk 1 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 0 optimal weight: 0.8980 chunk 24 optimal weight: 0.0670 chunk 26 optimal weight: 0.3980 chunk 34 optimal weight: 0.8980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.167614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.115335 restraints weight = 16846.689| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 3.01 r_work: 0.2982 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.205 8792 Z= 0.114 Angle : 0.542 12.226 11936 Z= 0.265 Chirality : 0.041 0.142 1386 Planarity : 0.004 0.039 1516 Dihedral : 5.507 82.406 1200 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.42 % Allowed : 14.38 % 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: 0.59 (0.25), residues: 1097 helix: 1.22 (0.23), residues: 522 sheet: -0.08 (0.31), residues: 246 loop : -0.40 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 602 HIS 0.003 0.001 HIS B 220 PHE 0.015 0.001 PHE A 141 TYR 0.018 0.001 TYR B 49 ARG 0.003 0.000 ARG A 593 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 485) hydrogen bonds : angle 4.32138 ( 1475) covalent geometry : bond 0.00269 ( 8791) covalent geometry : angle 0.54206 (11936) Misc. bond : bond 0.20454 ( 1) *********************** 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 130 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.6774 (OUTLIER) cc_final: 0.6421 (mp) REVERT: B 444 MET cc_start: 0.7885 (tpt) cc_final: 0.7587 (tpp) REVERT: B 454 TYR cc_start: 0.7783 (m-10) cc_final: 0.7556 (m-10) REVERT: B 599 MET cc_start: 0.6760 (ptp) cc_final: 0.6211 (ptt) outliers start: 13 outliers final: 10 residues processed: 125 average time/residue: 0.1897 time to fit residues: 34.0093 Evaluate side-chains 118 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 69 optimal weight: 0.4980 chunk 18 optimal weight: 0.0980 chunk 26 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.167712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.125651 restraints weight = 11295.772| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.07 r_work: 0.3093 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 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 = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.206 8792 Z= 0.118 Angle : 0.544 12.073 11936 Z= 0.267 Chirality : 0.041 0.139 1386 Planarity : 0.004 0.039 1516 Dihedral : 5.453 82.615 1200 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.96 % Allowed : 14.92 % Favored : 83.12 % 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: 1.35 (0.23), residues: 522 sheet: -0.12 (0.31), residues: 249 loop : -0.27 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 602 HIS 0.005 0.001 HIS B 524 PHE 0.014 0.001 PHE A 141 TYR 0.011 0.001 TYR A 145 ARG 0.004 0.000 ARG A 593 Details of bonding type rmsd hydrogen bonds : bond 0.03413 ( 485) hydrogen bonds : angle 4.26472 ( 1475) covalent geometry : bond 0.00281 ( 8791) covalent geometry : angle 0.54409 (11936) Misc. bond : bond 0.20616 ( 1) *********************** 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 132 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.6706 (OUTLIER) cc_final: 0.6331 (mp) REVERT: B 384 GLU cc_start: 0.7914 (tp30) cc_final: 0.7094 (tt0) REVERT: B 454 TYR cc_start: 0.7633 (m-10) cc_final: 0.7382 (m-10) REVERT: B 565 SER cc_start: 0.8638 (m) cc_final: 0.8348 (p) REVERT: B 599 MET cc_start: 0.6560 (ptp) cc_final: 0.6095 (ptt) outliers start: 18 outliers final: 15 residues processed: 126 average time/residue: 0.1938 time to fit residues: 35.1250 Evaluate side-chains 128 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 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 530 THR 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: 0.6980 chunk 80 optimal weight: 2.9990 chunk 97 optimal weight: 0.0270 chunk 102 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.167562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.126183 restraints weight = 14373.772| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 4.65 r_work: 0.2898 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 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 = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.207 8792 Z= 0.124 Angle : 0.547 12.257 11936 Z= 0.268 Chirality : 0.041 0.137 1386 Planarity : 0.004 0.039 1516 Dihedral : 5.439 82.636 1200 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.96 % Allowed : 15.47 % Favored : 82.57 % 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: 0.76 (0.26), residues: 1097 helix: 1.37 (0.23), residues: 522 sheet: -0.13 (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 0.004 0.001 HIS B 524 PHE 0.014 0.001 PHE A 162 TYR 0.011 0.001 TYR B 237 ARG 0.005 0.000 ARG A 593 Details of bonding type rmsd hydrogen bonds : bond 0.03420 ( 485) hydrogen bonds : angle 4.25709 ( 1475) covalent geometry : bond 0.00299 ( 8791) covalent geometry : angle 0.54701 (11936) Misc. bond : bond 0.20730 ( 1) *********************** 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 134 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 1.088 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.6749 (OUTLIER) cc_final: 0.6396 (mp) REVERT: B 384 GLU cc_start: 0.7968 (tp30) cc_final: 0.7142 (tt0) REVERT: B 454 TYR cc_start: 0.7661 (m-10) cc_final: 0.7407 (m-10) REVERT: B 565 SER cc_start: 0.8635 (m) cc_final: 0.8364 (p) REVERT: B 599 MET cc_start: 0.6528 (ptp) cc_final: 0.6063 (ptt) outliers start: 18 outliers final: 16 residues processed: 129 average time/residue: 0.2396 time to fit residues: 45.2075 Evaluate side-chains 130 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 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 530 THR 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: 5.9990 chunk 67 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 56 optimal weight: 0.4980 chunk 58 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 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 468 GLN ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.167945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.130291 restraints weight = 21956.476| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 6.05 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3357 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.206 8792 Z= 0.123 Angle : 0.544 12.290 11936 Z= 0.266 Chirality : 0.041 0.137 1386 Planarity : 0.004 0.039 1516 Dihedral : 5.426 82.438 1200 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.18 % Allowed : 15.58 % Favored : 82.24 % 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: 0.78 (0.26), residues: 1097 helix: 1.41 (0.23), residues: 520 sheet: -0.11 (0.31), residues: 249 loop : -0.24 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 602 HIS 0.004 0.001 HIS B 524 PHE 0.013 0.001 PHE A 162 TYR 0.011 0.001 TYR B 237 ARG 0.004 0.000 ARG A 593 Details of bonding type rmsd hydrogen bonds : bond 0.03409 ( 485) hydrogen bonds : angle 4.24218 ( 1475) covalent geometry : bond 0.00296 ( 8791) covalent geometry : angle 0.54425 (11936) Misc. bond : bond 0.20637 ( 1) *********************** 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 136 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.842 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7231 (mp) REVERT: B 328 MET cc_start: 0.7833 (ptp) cc_final: 0.7618 (mtt) REVERT: B 384 GLU cc_start: 0.7161 (tp30) cc_final: 0.6676 (tt0) REVERT: B 599 MET cc_start: 0.6853 (ptp) cc_final: 0.6432 (ptt) outliers start: 20 outliers final: 16 residues processed: 130 average time/residue: 0.1838 time to fit residues: 34.4802 Evaluate side-chains 131 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 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 530 THR 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: 3.9990 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.165660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.113724 restraints weight = 16642.060| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.19 r_work: 0.2950 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- 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: 0.7706 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.214 8792 Z= 0.153 Angle : 0.570 12.779 11936 Z= 0.278 Chirality : 0.042 0.143 1386 Planarity : 0.004 0.039 1516 Dihedral : 5.522 83.412 1200 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.96 % Allowed : 16.23 % Favored : 81.81 % 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: 1.31 (0.23), residues: 519 sheet: -0.11 (0.31), residues: 249 loop : -0.34 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 602 HIS 0.004 0.001 HIS B 524 PHE 0.013 0.001 PHE A 166 TYR 0.012 0.001 TYR B 135 ARG 0.004 0.000 ARG B 539 Details of bonding type rmsd hydrogen bonds : bond 0.03594 ( 485) hydrogen bonds : angle 4.29837 ( 1475) covalent geometry : bond 0.00376 ( 8791) covalent geometry : angle 0.57020 (11936) Misc. bond : bond 0.21368 ( 1) *********************** 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 129 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.6856 (OUTLIER) cc_final: 0.6500 (mp) REVERT: A 344 MET cc_start: 0.8546 (mmm) cc_final: 0.8328 (mmt) REVERT: B 384 GLU cc_start: 0.7943 (tp30) cc_final: 0.7171 (tt0) REVERT: B 599 MET cc_start: 0.6670 (ptp) cc_final: 0.6121 (ptt) outliers start: 18 outliers final: 16 residues processed: 124 average time/residue: 0.2056 time to fit residues: 36.3089 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 : 0.954 ------------------------------------------------------------------------------- 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 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 530 THR 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: 0.0040 chunk 89 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 28 optimal weight: 0.0570 chunk 91 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.3710 ------------------------------------------------------------------------------- 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** B 329 ASN 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 = 0.168929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.115155 restraints weight = 21738.232| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 3.83 r_work: 0.2945 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 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 = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.197 8792 Z= 0.108 Angle : 0.535 11.835 11936 Z= 0.262 Chirality : 0.041 0.137 1386 Planarity : 0.004 0.038 1516 Dihedral : 5.376 81.345 1200 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.96 % Allowed : 16.23 % Favored : 81.81 % 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: 0.89 (0.26), residues: 1097 helix: 1.53 (0.23), residues: 519 sheet: -0.08 (0.31), residues: 249 loop : -0.22 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 602 HIS 0.005 0.001 HIS B 524 PHE 0.013 0.001 PHE A 141 TYR 0.010 0.001 TYR B 237 ARG 0.004 0.000 ARG B 539 Details of bonding type rmsd hydrogen bonds : bond 0.03283 ( 485) hydrogen bonds : angle 4.20875 ( 1475) covalent geometry : bond 0.00250 ( 8791) covalent geometry : angle 0.53515 (11936) Misc. bond : bond 0.19719 ( 1) ********************** 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 133 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.6842 (OUTLIER) cc_final: 0.6519 (mp) REVERT: B 328 MET cc_start: 0.7605 (mtt) cc_final: 0.7144 (mtt) REVERT: B 599 MET cc_start: 0.6620 (ptp) cc_final: 0.6067 (ptt) outliers start: 18 outliers final: 15 residues processed: 128 average time/residue: 0.1912 time to fit residues: 35.2433 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 : 0.970 ------------------------------------------------------------------------------- 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 2 TYR Chi-restraints excluded: chain B residue 56 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 530 THR 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: 0.7980 chunk 107 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 39 optimal weight: 0.4980 chunk 105 optimal weight: 3.9990 chunk 61 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** B 563 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.167505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.115194 restraints weight = 16874.114| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 3.06 r_work: 0.2981 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.202 8792 Z= 0.122 Angle : 0.544 12.071 11936 Z= 0.266 Chirality : 0.041 0.138 1386 Planarity : 0.004 0.039 1516 Dihedral : 5.375 82.357 1200 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % 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: 0.87 (0.26), residues: 1097 helix: 1.48 (0.23), residues: 520 sheet: -0.07 (0.31), residues: 249 loop : -0.20 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 602 HIS 0.005 0.001 HIS B 524 PHE 0.013 0.001 PHE A 162 TYR 0.011 0.001 TYR B 237 ARG 0.005 0.000 ARG B 539 Details of bonding type rmsd hydrogen bonds : bond 0.03370 ( 485) hydrogen bonds : angle 4.21301 ( 1475) covalent geometry : bond 0.00293 ( 8791) covalent geometry : angle 0.54408 (11936) Misc. bond : bond 0.20188 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5038.87 seconds wall clock time: 87 minutes 34.61 seconds (5254.61 seconds total)