Starting phenix.real_space_refine on Tue Jul 29 04:51:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r8b_24314/07_2025/7r8b_24314.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r8b_24314/07_2025/7r8b_24314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r8b_24314/07_2025/7r8b_24314.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r8b_24314/07_2025/7r8b_24314.map" model { file = "/net/cci-nas-00/data/ceres_data/7r8b_24314/07_2025/7r8b_24314.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r8b_24314/07_2025/7r8b_24314.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.059 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: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 7027 2.51 5 N 1838 2.21 5 O 1936 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10868 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4626 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 22, 'TRANS': 565} Chain breaks: 3 Chain: "B" Number of atoms: 4482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4482 Classifications: {'peptide': 564} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 539} Chain breaks: 3 Chain: "C" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 901 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "D" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 803 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 100} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.23, per 1000 atoms: 0.57 Number of scatterers: 10868 At special positions: 0 Unit cell: (114.121, 105.791, 122.451, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 67 16.00 O 1936 8.00 N 1838 7.00 C 7027 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 587 " - pdb=" SG CYS A 600 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 117 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 108 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.3 seconds 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2540 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 9 sheets defined 52.9% alpha, 13.3% 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 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 91 through 101 Processing helix chain 'A' and resid 143 through 156 Processing helix chain 'A' and resid 160 through 175 removed outlier: 4.178A pdb=" N PHE A 164 " --> pdb=" O ASN A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.604A pdb=" N ALA A 181 " --> pdb=" O SER A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 208 Processing helix chain 'A' and resid 224 through 240 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 311 through 332 Processing helix chain 'A' and resid 332 through 347 removed outlier: 3.873A pdb=" N HIS A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 381 removed outlier: 3.604A pdb=" N LYS A 367 " --> pdb=" O GLY A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 405 removed outlier: 5.299A pdb=" N ASN A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LEU A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE A 403 " --> pdb=" O PHE A 399 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 454 Proline residue: A 431 - end of helix Proline residue: A 443 - end of helix removed outlier: 4.196A pdb=" N GLN A 454 " --> pdb=" O ASP A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 491 Proline residue: A 473 - end of helix removed outlier: 4.877A pdb=" N TRP A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 524 Proline residue: A 509 - end of helix Processing helix chain 'A' and resid 526 through 545 Processing helix chain 'A' and resid 556 through 563 Processing helix chain 'A' and resid 566 through 580 removed outlier: 4.272A pdb=" N TYR A 570 " --> pdb=" O THR A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 613 Processing helix chain 'A' and resid 614 through 618 removed outlier: 4.428A pdb=" N THR A 617 " --> pdb=" O PRO A 614 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER A 618 " --> pdb=" O GLY A 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 614 through 618' Processing helix chain 'A' and resid 619 through 646 removed outlier: 4.481A pdb=" N ILE A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) Proline residue: A 632 - end of helix Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 140 through 147 Processing helix chain 'B' and resid 162 through 175 Processing helix chain 'B' and resid 180 through 195 Processing helix chain 'B' and resid 197 through 201 removed outlier: 3.560A pdb=" N CYS B 200 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA B 201 " --> pdb=" O ARG B 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 197 through 201' Processing helix chain 'B' and resid 214 through 226 Processing helix chain 'B' and resid 244 through 261 Processing helix chain 'B' and resid 273 through 278 removed outlier: 3.600A pdb=" N ARG B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 306 removed outlier: 3.560A pdb=" N ALA B 306 " --> pdb=" O GLN B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 325 removed outlier: 3.750A pdb=" N THR B 325 " --> pdb=" O TYR B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 353 removed outlier: 4.046A pdb=" N LEU B 336 " --> pdb=" O ARG B 332 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA B 337 " --> pdb=" O GLU B 333 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 411 Processing helix chain 'B' and resid 413 through 435 Processing helix chain 'B' and resid 444 through 458 Processing helix chain 'B' and resid 459 through 473 Processing helix chain 'B' and resid 474 through 484 Processing helix chain 'B' and resid 490 through 513 removed outlier: 4.013A pdb=" N PHE B 494 " --> pdb=" O GLY B 490 " (cutoff:3.500A) Proline residue: B 502 - end of helix Processing helix chain 'B' and resid 514 through 516 No H-bonds generated for 'chain 'B' and resid 514 through 516' Processing helix chain 'B' and resid 525 through 553 Processing helix chain 'B' and resid 555 through 573 Processing helix chain 'B' and resid 585 through 593 Processing helix chain 'B' and resid 594 through 608 Processing helix chain 'B' and resid 627 through 633 removed outlier: 3.618A pdb=" N MET B 633 " --> pdb=" O ILE B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 665 Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'D' and resid 99 through 103 removed outlier: 3.907A pdb=" N LEU D 103 " --> pdb=" O SER D 100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 77 removed outlier: 5.875A pdb=" N LYS A 70 " --> pdb=" O TYR A 45 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N TYR A 45 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU A 74 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU A 41 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL A 76 " --> pdb=" O GLY A 39 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N GLY A 39 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ILE A 40 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N TYR A 114 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N HIS A 42 " --> pdb=" O GLU A 112 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N GLU A 112 " --> pdb=" O HIS A 42 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL A 113 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 132 removed outlier: 3.931A pdb=" N VAL A 245 " --> pdb=" O GLN A 80 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE A 273 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N SER A 267 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LEU A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 91 through 96 removed outlier: 7.485A pdb=" N PHE B 93 " --> pdb=" O ARG B 50 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ARG B 50 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N VAL B 95 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N GLU B 48 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 151 removed outlier: 6.390A pdb=" N LEU B 101 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N MET B 100 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LEU B 284 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA B 102 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N MET B 286 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE B 104 " --> pdb=" O MET B 286 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR B 293 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR B 287 " --> pdb=" O PRO B 291 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 26 Processing sheet with id=AA6, first strand: chain 'C' and resid 79 through 81 removed outlier: 6.698A pdb=" N TRP C 55 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL C 69 " --> pdb=" O MET C 53 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N MET C 53 " --> pdb=" O VAL C 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 24 through 27 Processing sheet with id=AA8, first strand: chain 'D' and resid 30 through 32 removed outlier: 6.561A pdb=" N LEU D 31 " --> pdb=" O GLU D 125 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLN D 57 " --> pdb=" O ARG D 66 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ARG D 66 " --> pdb=" O GLN D 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 30 through 32 removed outlier: 6.561A pdb=" N LEU D 31 " --> pdb=" O GLU D 125 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR D 117 " --> pdb=" O GLN D 110 " (cutoff:3.500A) 603 hydrogen bonds defined for protein. 1749 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: 3.02 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3453 1.34 - 1.46: 2633 1.46 - 1.58: 4913 1.58 - 1.70: 0 1.70 - 1.82: 107 Bond restraints: 11106 Sorted by residual: bond pdb=" C PHE A 442 " pdb=" N PRO A 443 " ideal model delta sigma weight residual 1.334 1.366 -0.032 1.51e-02 4.39e+03 4.49e+00 bond pdb=" CA LYS B 126 " pdb=" CB LYS B 126 " ideal model delta sigma weight residual 1.526 1.545 -0.020 1.68e-02 3.54e+03 1.37e+00 bond pdb=" C ILE B 459 " pdb=" N PRO B 460 " ideal model delta sigma weight residual 1.335 1.349 -0.014 1.28e-02 6.10e+03 1.25e+00 bond pdb=" C3 CLR A 701 " pdb=" O1 CLR A 701 " ideal model delta sigma weight residual 1.413 1.391 0.022 2.00e-02 2.50e+03 1.24e+00 bond pdb=" CA THR A 430 " pdb=" C THR A 430 " ideal model delta sigma weight residual 1.520 1.533 -0.013 1.23e-02 6.61e+03 1.08e+00 ... (remaining 11101 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 14648 1.41 - 2.82: 306 2.82 - 4.24: 59 4.24 - 5.65: 19 5.65 - 7.06: 9 Bond angle restraints: 15041 Sorted by residual: angle pdb=" C PRO A 556 " pdb=" N ILE A 557 " pdb=" CA ILE A 557 " ideal model delta sigma weight residual 120.33 123.55 -3.22 8.00e-01 1.56e+00 1.62e+01 angle pdb=" C VAL A 404 " pdb=" N LEU A 405 " pdb=" CA LEU A 405 " ideal model delta sigma weight residual 121.54 128.47 -6.93 1.91e+00 2.74e-01 1.32e+01 angle pdb=" C ALA D 70 " pdb=" N ALA D 71 " pdb=" CA ALA D 71 " ideal model delta sigma weight residual 121.54 128.02 -6.48 1.91e+00 2.74e-01 1.15e+01 angle pdb=" N VAL B 205 " pdb=" CA VAL B 205 " pdb=" C VAL B 205 " ideal model delta sigma weight residual 111.91 109.05 2.86 8.90e-01 1.26e+00 1.04e+01 angle pdb=" N ILE B 292 " pdb=" CA ILE B 292 " pdb=" C ILE B 292 " ideal model delta sigma weight residual 111.90 109.40 2.50 8.10e-01 1.52e+00 9.53e+00 ... (remaining 15036 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 6087 17.40 - 34.81: 494 34.81 - 52.21: 95 52.21 - 69.61: 29 69.61 - 87.02: 7 Dihedral angle restraints: 6712 sinusoidal: 2754 harmonic: 3958 Sorted by residual: dihedral pdb=" CB ARG A 198 " pdb=" CG ARG A 198 " pdb=" CD ARG A 198 " pdb=" NE ARG A 198 " ideal model delta sinusoidal sigma weight residual 60.00 119.50 -59.50 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N ARG A 122 " pdb=" CA ARG A 122 " pdb=" CB ARG A 122 " pdb=" CG ARG A 122 " ideal model delta sinusoidal sigma weight residual -60.00 -118.56 58.56 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB MET B 558 " pdb=" CG MET B 558 " pdb=" SD MET B 558 " pdb=" CE MET B 558 " ideal model delta sinusoidal sigma weight residual -60.00 -2.80 -57.20 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 6709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1597 0.072 - 0.143: 112 0.143 - 0.215: 2 0.215 - 0.286: 3 0.286 - 0.358: 2 Chirality restraints: 1716 Sorted by residual: chirality pdb=" C14 CLR B 801 " pdb=" C13 CLR B 801 " pdb=" C15 CLR B 801 " pdb=" C8 CLR B 801 " both_signs ideal model delta sigma weight residual False -2.32 -2.68 0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" C14 CLR A 701 " pdb=" C13 CLR A 701 " pdb=" C15 CLR A 701 " pdb=" C8 CLR A 701 " both_signs ideal model delta sigma weight residual False -2.32 -2.64 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" C9 CLR B 801 " pdb=" C10 CLR B 801 " pdb=" C11 CLR B 801 " pdb=" C8 CLR B 801 " both_signs ideal model delta sigma weight residual False -2.45 -2.69 0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 1713 not shown) Planarity restraints: 1884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 490 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO B 491 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 491 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 491 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 276 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO A 277 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 277 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 277 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 126 " -0.006 2.00e-02 2.50e+03 1.13e-02 1.28e+00 pdb=" C LYS B 126 " 0.020 2.00e-02 2.50e+03 pdb=" O LYS B 126 " -0.007 2.00e-02 2.50e+03 pdb=" N ILE B 127 " -0.007 2.00e-02 2.50e+03 ... (remaining 1881 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 154 2.66 - 3.22: 9864 3.22 - 3.78: 16807 3.78 - 4.34: 22984 4.34 - 4.90: 38658 Nonbonded interactions: 88467 Sorted by model distance: nonbonded pdb=" OG SER D 27 " pdb=" OG1 THR D 42 " model vdw 2.103 3.040 nonbonded pdb=" O VAL A 542 " pdb=" OG SER A 546 " model vdw 2.204 3.040 nonbonded pdb=" OG SER D 83 " pdb=" OG1 THR D 94 " model vdw 2.258 3.040 nonbonded pdb=" O ASN A 410 " pdb=" OG1 THR A 586 " model vdw 2.267 3.040 nonbonded pdb=" NE ARG A 550 " pdb=" O LEU B 434 " model vdw 2.290 3.120 ... (remaining 88462 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=1.00 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: 1.550 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.950 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 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 : 0.002 0.032 11109 Z= 0.115 Angle : 0.553 7.058 15047 Z= 0.314 Chirality : 0.040 0.358 1716 Planarity : 0.003 0.035 1884 Dihedral : 13.495 87.019 4163 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.94 % Allowed : 18.92 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: -1.73 (0.21), residues: 1351 helix: 0.06 (0.18), residues: 702 sheet: -1.48 (0.35), residues: 182 loop : -2.85 (0.25), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 584 HIS 0.003 0.000 HIS B 531 PHE 0.006 0.001 PHE A 502 TYR 0.007 0.001 TYR C 115 ARG 0.003 0.000 ARG B 329 Details of bonding type rmsd hydrogen bonds : bond 0.12519 ( 599) hydrogen bonds : angle 5.17450 ( 1749) SS BOND : bond 0.00173 ( 3) SS BOND : angle 0.12424 ( 6) covalent geometry : bond 0.00202 (11106) covalent geometry : angle 0.55279 (15041) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 210 time to evaluate : 2.544 Fit side-chains REVERT: A 118 ARG cc_start: 0.7989 (mpt180) cc_final: 0.7713 (mmt90) REVERT: A 134 GLN cc_start: 0.7281 (tt0) cc_final: 0.6876 (tm-30) REVERT: A 313 GLU cc_start: 0.7240 (tm-30) cc_final: 0.6878 (tm-30) REVERT: A 437 ASN cc_start: 0.7595 (m-40) cc_final: 0.7357 (m110) REVERT: A 523 ILE cc_start: 0.7575 (tp) cc_final: 0.7314 (tp) REVERT: A 553 GLN cc_start: 0.8461 (mm-40) cc_final: 0.8218 (mm110) REVERT: B 446 MET cc_start: 0.7227 (mmt) cc_final: 0.7018 (mmt) REVERT: C 86 LYS cc_start: 0.8507 (tttp) cc_final: 0.8245 (ttmt) REVERT: C 101 TYR cc_start: 0.8674 (m-80) cc_final: 0.8163 (m-80) REVERT: D 90 ASP cc_start: 0.7779 (m-30) cc_final: 0.7572 (m-30) REVERT: D 99 GLU cc_start: 0.8270 (mp0) cc_final: 0.7320 (mp0) outliers start: 23 outliers final: 11 residues processed: 227 average time/residue: 0.3211 time to fit residues: 100.7381 Evaluate side-chains 154 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 112 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 179 HIS A 206 GLN A 230 GLN A 347 HIS A 454 GLN A 462 GLN ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN A 597 ASN A 604 GLN A 607 GLN B 43 GLN B 99 GLN B 135 ASN B 153 GLN B 172 GLN B 250 ASN B 262 ASN B 271 GLN B 438 HIS B 526 GLN ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN C 75 ASN D 58 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.112853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.085566 restraints weight = 15625.564| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.26 r_work: 0.2808 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11109 Z= 0.161 Angle : 0.576 9.668 15047 Z= 0.288 Chirality : 0.042 0.242 1716 Planarity : 0.004 0.036 1884 Dihedral : 5.322 47.636 1646 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.63 % Allowed : 18.16 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.23), residues: 1351 helix: 1.15 (0.19), residues: 707 sheet: -0.98 (0.36), residues: 190 loop : -2.26 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 584 HIS 0.005 0.001 HIS B 531 PHE 0.016 0.001 PHE B 595 TYR 0.019 0.001 TYR D 111 ARG 0.006 0.001 ARG A 550 Details of bonding type rmsd hydrogen bonds : bond 0.04050 ( 599) hydrogen bonds : angle 3.85120 ( 1749) SS BOND : bond 0.00242 ( 3) SS BOND : angle 0.43026 ( 6) covalent geometry : bond 0.00382 (11106) covalent geometry : angle 0.57583 (15041) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 149 time to evaluate : 1.066 Fit side-chains REVERT: B 50 ARG cc_start: 0.7846 (ttp-170) cc_final: 0.7606 (ttm170) REVERT: B 116 ASP cc_start: 0.8565 (m-30) cc_final: 0.8304 (m-30) REVERT: B 319 ASP cc_start: 0.8220 (m-30) cc_final: 0.7990 (m-30) REVERT: C 65 GLU cc_start: 0.8744 (tt0) cc_final: 0.8531 (tt0) REVERT: C 86 LYS cc_start: 0.8764 (tttp) cc_final: 0.8502 (ttmt) REVERT: C 101 TYR cc_start: 0.8971 (m-80) cc_final: 0.8450 (m-80) REVERT: D 75 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7708 (m-30) REVERT: D 99 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7136 (mp0) outliers start: 43 outliers final: 26 residues processed: 180 average time/residue: 0.2424 time to fit residues: 61.3804 Evaluate side-chains 163 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 117 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 12 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS B 150 HIS B 172 GLN ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.107504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.080284 restraints weight = 15749.025| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.22 r_work: 0.2721 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11109 Z= 0.204 Angle : 0.581 8.503 15047 Z= 0.294 Chirality : 0.043 0.182 1716 Planarity : 0.004 0.037 1884 Dihedral : 4.994 46.065 1637 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.73 % Allowed : 16.55 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.01 (0.23), residues: 1351 helix: 1.43 (0.20), residues: 706 sheet: -0.84 (0.36), residues: 197 loop : -1.94 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 584 HIS 0.003 0.001 HIS B 531 PHE 0.016 0.002 PHE B 461 TYR 0.017 0.002 TYR D 111 ARG 0.005 0.000 ARG A 550 Details of bonding type rmsd hydrogen bonds : bond 0.04592 ( 599) hydrogen bonds : angle 3.93252 ( 1749) SS BOND : bond 0.00676 ( 3) SS BOND : angle 0.38645 ( 6) covalent geometry : bond 0.00493 (11106) covalent geometry : angle 0.58061 (15041) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 132 time to evaluate : 1.772 Fit side-chains revert: symmetry clash REVERT: A 313 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7494 (tm-30) REVERT: A 353 MET cc_start: 0.7319 (pmm) cc_final: 0.7104 (pmm) REVERT: A 599 MET cc_start: 0.7984 (mpp) cc_final: 0.7760 (mpp) REVERT: B 116 ASP cc_start: 0.8539 (m-30) cc_final: 0.8312 (m-30) REVERT: B 214 SER cc_start: 0.8070 (OUTLIER) cc_final: 0.7869 (p) REVERT: C 32 GLN cc_start: 0.8926 (mp10) cc_final: 0.8722 (mp10) REVERT: C 86 LYS cc_start: 0.8709 (tttp) cc_final: 0.8269 (ttmt) REVERT: C 101 TYR cc_start: 0.9042 (m-80) cc_final: 0.8497 (m-80) REVERT: D 99 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7261 (mp0) outliers start: 56 outliers final: 35 residues processed: 177 average time/residue: 0.2894 time to fit residues: 73.1009 Evaluate side-chains 164 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 117 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 118 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** 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 = 0.3303 r_free = 0.3303 target = 0.109977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.082814 restraints weight = 15580.239| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.23 r_work: 0.2762 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11109 Z= 0.124 Angle : 0.536 11.741 15047 Z= 0.267 Chirality : 0.040 0.191 1716 Planarity : 0.003 0.034 1884 Dihedral : 4.933 49.806 1637 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.38 % Allowed : 18.07 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.47 (0.24), residues: 1351 helix: 1.79 (0.20), residues: 704 sheet: -0.61 (0.37), residues: 191 loop : -1.68 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 461 HIS 0.004 0.000 HIS B 531 PHE 0.023 0.001 PHE C 89 TYR 0.012 0.001 TYR D 111 ARG 0.003 0.000 ARG A 118 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 599) hydrogen bonds : angle 3.82900 ( 1749) SS BOND : bond 0.00247 ( 3) SS BOND : angle 0.27789 ( 6) covalent geometry : bond 0.00288 (11106) covalent geometry : angle 0.53635 (15041) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 time to evaluate : 1.237 Fit side-chains revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8250 (mmt90) cc_final: 0.7970 (mmt90) REVERT: A 134 GLN cc_start: 0.7944 (tt0) cc_final: 0.7415 (pt0) REVERT: A 313 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7408 (tm-30) REVERT: A 599 MET cc_start: 0.7807 (mpp) cc_final: 0.7524 (mpp) REVERT: B 50 ARG cc_start: 0.7736 (ttp-170) cc_final: 0.7422 (ttm110) REVERT: B 116 ASP cc_start: 0.8503 (m-30) cc_final: 0.8250 (m-30) REVERT: B 477 MET cc_start: 0.9129 (ttp) cc_final: 0.8908 (ttp) REVERT: C 32 GLN cc_start: 0.8924 (mp10) cc_final: 0.8705 (mp10) REVERT: C 86 LYS cc_start: 0.8693 (tttp) cc_final: 0.8274 (ttmt) REVERT: C 101 TYR cc_start: 0.8971 (m-80) cc_final: 0.8462 (m-80) REVERT: D 99 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7231 (mp0) outliers start: 40 outliers final: 32 residues processed: 162 average time/residue: 0.2642 time to fit residues: 59.4679 Evaluate side-chains 161 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 584 TRP Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 117 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 15 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 86 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS B 199 GLN ** B 568 ASN ** 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 = 0.3249 r_free = 0.3249 target = 0.106177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.078973 restraints weight = 15672.036| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.21 r_work: 0.2684 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11109 Z= 0.222 Angle : 0.603 11.511 15047 Z= 0.302 Chirality : 0.044 0.190 1716 Planarity : 0.004 0.037 1884 Dihedral : 5.040 48.494 1637 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.39 % Allowed : 17.06 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.24), residues: 1351 helix: 1.76 (0.20), residues: 700 sheet: -0.65 (0.36), residues: 197 loop : -1.75 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 584 HIS 0.004 0.001 HIS B 531 PHE 0.015 0.002 PHE B 461 TYR 0.018 0.002 TYR B 571 ARG 0.004 0.000 ARG A 550 Details of bonding type rmsd hydrogen bonds : bond 0.04728 ( 599) hydrogen bonds : angle 4.01027 ( 1749) SS BOND : bond 0.00293 ( 3) SS BOND : angle 0.27914 ( 6) covalent geometry : bond 0.00540 (11106) covalent geometry : angle 0.60334 (15041) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 123 time to evaluate : 1.179 Fit side-chains revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8264 (mmt90) cc_final: 0.7915 (mmt90) REVERT: A 134 GLN cc_start: 0.8071 (tt0) cc_final: 0.7448 (pt0) REVERT: A 313 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7544 (tm-30) REVERT: B 116 ASP cc_start: 0.8577 (m-30) cc_final: 0.8344 (m-30) REVERT: C 32 GLN cc_start: 0.8951 (mp10) cc_final: 0.8735 (mp10) REVERT: C 86 LYS cc_start: 0.8700 (tttp) cc_final: 0.8293 (ttmt) REVERT: C 101 TYR cc_start: 0.9033 (m-80) cc_final: 0.8483 (m-80) REVERT: D 37 GLU cc_start: 0.8455 (pm20) cc_final: 0.8201 (pm20) REVERT: D 99 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7251 (mp0) outliers start: 52 outliers final: 42 residues processed: 166 average time/residue: 0.2709 time to fit residues: 63.5661 Evaluate side-chains 166 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 123 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 584 TRP Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 117 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 24 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** 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 = 0.3297 r_free = 0.3297 target = 0.109531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.082623 restraints weight = 15666.180| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.21 r_work: 0.2753 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11109 Z= 0.120 Angle : 0.537 13.271 15047 Z= 0.267 Chirality : 0.040 0.183 1716 Planarity : 0.003 0.033 1884 Dihedral : 4.957 53.539 1637 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.72 % Allowed : 17.65 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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 (0.24), residues: 1351 helix: 2.03 (0.20), residues: 700 sheet: -0.50 (0.37), residues: 197 loop : -1.60 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 461 HIS 0.004 0.001 HIS B 531 PHE 0.011 0.001 PHE C 89 TYR 0.015 0.001 TYR B 571 ARG 0.003 0.000 ARG B 26 Details of bonding type rmsd hydrogen bonds : bond 0.03755 ( 599) hydrogen bonds : angle 3.81833 ( 1749) SS BOND : bond 0.00265 ( 3) SS BOND : angle 0.26872 ( 6) covalent geometry : bond 0.00279 (11106) covalent geometry : angle 0.53672 (15041) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 129 time to evaluate : 1.331 Fit side-chains revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8168 (mmt90) cc_final: 0.7823 (mmt90) REVERT: A 134 GLN cc_start: 0.7984 (tt0) cc_final: 0.7473 (pt0) REVERT: A 313 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7396 (tm-30) REVERT: B 116 ASP cc_start: 0.8528 (m-30) cc_final: 0.8259 (m-30) REVERT: B 208 MET cc_start: 0.7052 (pp-130) cc_final: 0.6781 (ppp) REVERT: B 343 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8508 (tp40) REVERT: B 477 MET cc_start: 0.9133 (ttp) cc_final: 0.8917 (ttp) REVERT: C 32 GLN cc_start: 0.8950 (mp10) cc_final: 0.8736 (mp10) REVERT: C 53 MET cc_start: 0.8921 (mmm) cc_final: 0.8705 (mmm) REVERT: C 86 LYS cc_start: 0.8707 (tttp) cc_final: 0.8318 (ttmt) REVERT: C 101 TYR cc_start: 0.8953 (m-80) cc_final: 0.8423 (m-80) REVERT: D 37 GLU cc_start: 0.8464 (pm20) cc_final: 0.8263 (pm20) REVERT: D 99 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7251 (mp0) outliers start: 44 outliers final: 35 residues processed: 164 average time/residue: 0.3711 time to fit residues: 83.7023 Evaluate side-chains 162 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 126 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 584 TRP Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 117 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 126 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 73 optimal weight: 0.0770 chunk 35 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 83 optimal weight: 0.0010 chunk 64 optimal weight: 3.9990 overall best weight: 1.0148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** 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 = 0.3293 r_free = 0.3293 target = 0.109253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.082451 restraints weight = 15822.389| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.19 r_work: 0.2750 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11109 Z= 0.132 Angle : 0.550 12.661 15047 Z= 0.273 Chirality : 0.041 0.211 1716 Planarity : 0.003 0.033 1884 Dihedral : 4.921 54.967 1637 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.72 % Allowed : 17.82 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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 (0.24), residues: 1351 helix: 2.09 (0.20), residues: 700 sheet: -0.46 (0.37), residues: 186 loop : -1.55 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 461 HIS 0.004 0.000 HIS B 531 PHE 0.037 0.001 PHE C 89 TYR 0.015 0.001 TYR B 571 ARG 0.004 0.000 ARG B 26 Details of bonding type rmsd hydrogen bonds : bond 0.03864 ( 599) hydrogen bonds : angle 3.81216 ( 1749) SS BOND : bond 0.00198 ( 3) SS BOND : angle 0.29561 ( 6) covalent geometry : bond 0.00309 (11106) covalent geometry : angle 0.54987 (15041) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 124 time to evaluate : 1.115 Fit side-chains revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8110 (mmt90) cc_final: 0.7840 (mmt90) REVERT: A 134 GLN cc_start: 0.8005 (tt0) cc_final: 0.7488 (pt0) REVERT: A 302 MET cc_start: 0.8673 (tpp) cc_final: 0.8453 (mmm) REVERT: A 313 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7408 (tm-30) REVERT: B 116 ASP cc_start: 0.8492 (m-30) cc_final: 0.8231 (m-30) REVERT: B 208 MET cc_start: 0.7019 (pp-130) cc_final: 0.6731 (ppp) REVERT: C 32 GLN cc_start: 0.8963 (mp10) cc_final: 0.8735 (mp10) REVERT: C 53 MET cc_start: 0.8968 (mmm) cc_final: 0.8765 (mmm) REVERT: C 86 LYS cc_start: 0.8641 (tttp) cc_final: 0.8251 (ttmt) REVERT: C 101 TYR cc_start: 0.8925 (m-80) cc_final: 0.8402 (m-80) REVERT: D 37 GLU cc_start: 0.8492 (pm20) cc_final: 0.8278 (pm20) REVERT: D 99 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7171 (mp0) outliers start: 44 outliers final: 40 residues processed: 159 average time/residue: 0.2730 time to fit residues: 60.7612 Evaluate side-chains 164 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 584 TRP Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 117 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 89 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.107368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.080724 restraints weight = 15665.652| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.16 r_work: 0.2723 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11109 Z= 0.175 Angle : 0.586 14.195 15047 Z= 0.289 Chirality : 0.042 0.194 1716 Planarity : 0.004 0.034 1884 Dihedral : 4.970 55.502 1637 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.14 % Allowed : 17.65 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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 (0.24), residues: 1351 helix: 2.03 (0.20), residues: 701 sheet: -0.45 (0.37), residues: 186 loop : -1.53 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 461 HIS 0.004 0.001 HIS B 531 PHE 0.026 0.001 PHE C 89 TYR 0.015 0.001 TYR B 571 ARG 0.004 0.000 ARG B 26 Details of bonding type rmsd hydrogen bonds : bond 0.04283 ( 599) hydrogen bonds : angle 3.89772 ( 1749) SS BOND : bond 0.00253 ( 3) SS BOND : angle 0.27139 ( 6) covalent geometry : bond 0.00425 (11106) covalent geometry : angle 0.58586 (15041) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 124 time to evaluate : 1.284 Fit side-chains revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8140 (mmt90) cc_final: 0.7847 (mmt90) REVERT: A 134 GLN cc_start: 0.8146 (tt0) cc_final: 0.7507 (pt0) REVERT: A 302 MET cc_start: 0.8687 (tpp) cc_final: 0.8445 (mmm) REVERT: A 313 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7449 (tm-30) REVERT: A 480 MET cc_start: 0.8935 (tpp) cc_final: 0.8636 (mmm) REVERT: B 208 MET cc_start: 0.7017 (pp-130) cc_final: 0.6715 (ppp) REVERT: C 86 LYS cc_start: 0.8673 (tttp) cc_final: 0.8291 (ttmt) REVERT: C 101 TYR cc_start: 0.8978 (m-80) cc_final: 0.8390 (m-80) REVERT: D 99 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7215 (mp0) outliers start: 49 outliers final: 41 residues processed: 162 average time/residue: 0.2590 time to fit residues: 58.5589 Evaluate side-chains 164 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 122 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 584 TRP Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 117 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 54 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 58 optimal weight: 0.0770 chunk 84 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.110529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.083962 restraints weight = 15737.962| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.17 r_work: 0.2764 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11109 Z= 0.112 Angle : 0.549 14.545 15047 Z= 0.271 Chirality : 0.040 0.190 1716 Planarity : 0.003 0.032 1884 Dihedral : 4.921 59.726 1637 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.29 % Allowed : 18.24 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.24), residues: 1351 helix: 2.18 (0.20), residues: 700 sheet: -0.43 (0.36), residues: 197 loop : -1.36 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 461 HIS 0.005 0.001 HIS B 531 PHE 0.017 0.001 PHE C 89 TYR 0.014 0.001 TYR B 571 ARG 0.004 0.000 ARG B 26 Details of bonding type rmsd hydrogen bonds : bond 0.03623 ( 599) hydrogen bonds : angle 3.78070 ( 1749) SS BOND : bond 0.00179 ( 3) SS BOND : angle 0.29350 ( 6) covalent geometry : bond 0.00253 (11106) covalent geometry : angle 0.54869 (15041) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 1.230 Fit side-chains revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8102 (mmt90) cc_final: 0.7815 (mmt90) REVERT: A 134 GLN cc_start: 0.8071 (tt0) cc_final: 0.7489 (pt0) REVERT: A 302 MET cc_start: 0.8672 (tpp) cc_final: 0.8462 (mmm) REVERT: A 313 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7370 (tm-30) REVERT: B 208 MET cc_start: 0.6980 (pp-130) cc_final: 0.6681 (ppp) REVERT: B 477 MET cc_start: 0.9107 (ttp) cc_final: 0.8877 (ttp) REVERT: C 86 LYS cc_start: 0.8626 (tttp) cc_final: 0.8213 (ttmt) REVERT: D 99 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7239 (mp0) outliers start: 39 outliers final: 35 residues processed: 158 average time/residue: 0.2785 time to fit residues: 61.6683 Evaluate side-chains 159 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 584 TRP Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS ** B 568 ASN ** 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 = 0.3286 r_free = 0.3286 target = 0.108017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.080590 restraints weight = 15812.124| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.30 r_work: 0.2720 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11109 Z= 0.166 Angle : 0.581 14.380 15047 Z= 0.288 Chirality : 0.042 0.184 1716 Planarity : 0.004 0.033 1884 Dihedral : 4.909 59.610 1636 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.21 % Allowed : 18.50 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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 (0.24), residues: 1351 helix: 2.07 (0.20), residues: 704 sheet: -0.42 (0.36), residues: 197 loop : -1.36 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 461 HIS 0.004 0.001 HIS B 531 PHE 0.022 0.001 PHE C 89 TYR 0.022 0.001 TYR B 571 ARG 0.004 0.000 ARG A 253 Details of bonding type rmsd hydrogen bonds : bond 0.04154 ( 599) hydrogen bonds : angle 3.86002 ( 1749) SS BOND : bond 0.00215 ( 3) SS BOND : angle 0.33100 ( 6) covalent geometry : bond 0.00403 (11106) covalent geometry : angle 0.58091 (15041) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 121 time to evaluate : 1.128 Fit side-chains revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8091 (mmt90) cc_final: 0.7791 (mmt90) REVERT: A 134 GLN cc_start: 0.8158 (tt0) cc_final: 0.7504 (pt0) REVERT: A 302 MET cc_start: 0.8711 (tpp) cc_final: 0.8492 (mmm) REVERT: A 313 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7443 (tm-30) REVERT: B 208 MET cc_start: 0.6964 (pp-130) cc_final: 0.6652 (ppp) REVERT: C 86 LYS cc_start: 0.8660 (tttp) cc_final: 0.8271 (ttmt) REVERT: D 99 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7158 (mp0) outliers start: 38 outliers final: 37 residues processed: 152 average time/residue: 0.2651 time to fit residues: 56.3006 Evaluate side-chains 158 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 120 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 584 TRP Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 89 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 120 optimal weight: 0.5980 chunk 100 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** 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 = 0.3315 r_free = 0.3315 target = 0.110117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.082840 restraints weight = 15747.163| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.31 r_work: 0.2751 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11109 Z= 0.114 Angle : 0.555 14.455 15047 Z= 0.275 Chirality : 0.040 0.187 1716 Planarity : 0.003 0.033 1884 Dihedral : 4.841 57.150 1636 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.29 % Allowed : 18.41 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 1.01 (0.24), residues: 1351 helix: 2.19 (0.20), residues: 700 sheet: -0.30 (0.37), residues: 185 loop : -1.33 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 461 HIS 0.005 0.000 HIS B 531 PHE 0.011 0.001 PHE B 595 TYR 0.021 0.001 TYR B 571 ARG 0.004 0.000 ARG B 26 Details of bonding type rmsd hydrogen bonds : bond 0.03678 ( 599) hydrogen bonds : angle 3.80197 ( 1749) SS BOND : bond 0.00177 ( 3) SS BOND : angle 0.31788 ( 6) covalent geometry : bond 0.00261 (11106) covalent geometry : angle 0.55465 (15041) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5900.25 seconds wall clock time: 104 minutes 21.03 seconds (6261.03 seconds total)