Starting phenix.real_space_refine on Wed Feb 4 13:23:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r8b_24314/02_2026/7r8b_24314.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r8b_24314/02_2026/7r8b_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_24314/02_2026/7r8b_24314.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r8b_24314/02_2026/7r8b_24314.map" model { file = "/net/cci-nas-00/data/ceres_data/7r8b_24314/02_2026/7r8b_24314.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r8b_24314/02_2026/7r8b_24314.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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: 2.33, per 1000 atoms: 0.21 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: 0.86 Conformation dependent library (CDL) restraints added in 404.0 milliseconds 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: 0.35 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: 1.59 Time building geometry restraints manager: 1.16 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.620 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.250 ------------------------------------------------------------------------------- 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 : 6.62 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.003 0.000 ARG B 329 TYR 0.007 0.001 TYR C 115 PHE 0.006 0.001 PHE A 502 TRP 0.005 0.001 TRP B 584 HIS 0.003 0.000 HIS B 531 Details of bonding type rmsd covalent geometry : bond 0.00202 (11106) covalent geometry : angle 0.55279 (15041) SS BOND : bond 0.00173 ( 3) SS BOND : angle 0.12424 ( 6) hydrogen bonds : bond 0.12519 ( 599) hydrogen bonds : angle 5.17450 ( 1749) *********************** 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 : 0.282 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: 0.1090 time to fit residues: 33.9950 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 : 0.300 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN 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 A 578 ASN A 597 ASN A 604 GLN A 607 GLN B 43 GLN B 99 GLN B 135 ASN B 150 HIS 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: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.109075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.081689 restraints weight = 15695.605| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.25 r_work: 0.2732 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2252 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= 0.215 Angle : 0.620 9.585 15047 Z= 0.311 Chirality : 0.044 0.239 1716 Planarity : 0.004 0.037 1884 Dihedral : 5.395 45.583 1646 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.56 % Allowed : 17.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.23), residues: 1351 helix: 1.02 (0.19), residues: 705 sheet: -1.11 (0.35), residues: 197 loop : -2.32 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 550 TYR 0.020 0.002 TYR D 111 PHE 0.019 0.002 PHE B 595 TRP 0.013 0.002 TRP B 584 HIS 0.004 0.001 HIS B 531 Details of bonding type rmsd covalent geometry : bond 0.00519 (11106) covalent geometry : angle 0.62006 (15041) SS BOND : bond 0.00761 ( 3) SS BOND : angle 0.47621 ( 6) hydrogen bonds : bond 0.04692 ( 599) hydrogen bonds : angle 3.99608 ( 1749) *********************** 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 197 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 143 time to evaluate : 0.473 Fit side-chains REVERT: B 116 ASP cc_start: 0.8536 (m-30) cc_final: 0.8283 (m-30) REVERT: B 319 ASP cc_start: 0.8276 (m-30) cc_final: 0.8076 (m-30) REVERT: C 101 TYR cc_start: 0.9020 (m-80) cc_final: 0.8519 (m-80) REVERT: D 75 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7758 (m-30) REVERT: D 99 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7208 (mp0) outliers start: 54 outliers final: 34 residues processed: 185 average time/residue: 0.1044 time to fit residues: 27.3462 Evaluate side-chains 165 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 225 CYS 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 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 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 75 ASP Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 126 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 76 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 597 ASN ** 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 = 0.3300 r_free = 0.3300 target = 0.109571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.082424 restraints weight = 15648.560| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.23 r_work: 0.2755 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11109 Z= 0.152 Angle : 0.542 8.208 15047 Z= 0.274 Chirality : 0.041 0.176 1716 Planarity : 0.003 0.036 1884 Dihedral : 5.025 47.155 1639 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.74 % Favored : 95.19 % Rotamer: Outliers : 3.55 % Allowed : 17.57 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.23), residues: 1351 helix: 1.50 (0.20), residues: 706 sheet: -0.76 (0.37), residues: 190 loop : -1.95 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 198 TYR 0.015 0.001 TYR D 111 PHE 0.015 0.001 PHE B 595 TRP 0.009 0.001 TRP B 584 HIS 0.004 0.001 HIS B 531 Details of bonding type rmsd covalent geometry : bond 0.00363 (11106) covalent geometry : angle 0.54249 (15041) SS BOND : bond 0.00452 ( 3) SS BOND : angle 0.37452 ( 6) hydrogen bonds : bond 0.04070 ( 599) hydrogen bonds : angle 3.85017 ( 1749) *********************** 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 173 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 131 time to evaluate : 0.394 Fit side-chains REVERT: A 118 ARG cc_start: 0.8268 (mmt90) cc_final: 0.8004 (mmt90) REVERT: A 313 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7448 (tm-30) REVERT: A 597 ASN cc_start: 0.7593 (OUTLIER) cc_final: 0.7205 (m-40) REVERT: A 599 MET cc_start: 0.7981 (mpp) cc_final: 0.7747 (mpp) REVERT: B 50 ARG cc_start: 0.7676 (ttp-170) cc_final: 0.7454 (ttm110) REVERT: B 116 ASP cc_start: 0.8528 (m-30) cc_final: 0.8289 (m-30) REVERT: B 319 ASP cc_start: 0.8325 (m-30) cc_final: 0.8043 (m-30) REVERT: C 32 GLN cc_start: 0.8916 (mp10) cc_final: 0.8714 (mp10) REVERT: C 101 TYR cc_start: 0.9005 (m-80) cc_final: 0.8443 (m-80) REVERT: D 99 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7213 (mp0) outliers start: 42 outliers final: 25 residues processed: 161 average time/residue: 0.1079 time to fit residues: 24.4790 Evaluate side-chains 156 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 597 ASN Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 200 CYS 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 444 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 40 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 99 GLU Chi-restraints excluded: chain D residue 103 LEU 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 70 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 55 optimal weight: 0.1980 chunk 78 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 597 ASN ** 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 = 0.3307 r_free = 0.3307 target = 0.110090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.082978 restraints weight = 15694.959| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.23 r_work: 0.2758 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11109 Z= 0.131 Angle : 0.533 10.245 15047 Z= 0.267 Chirality : 0.040 0.183 1716 Planarity : 0.003 0.035 1884 Dihedral : 4.930 49.740 1638 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.05 % Allowed : 17.15 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.24), residues: 1351 helix: 1.79 (0.20), residues: 704 sheet: -0.70 (0.36), residues: 197 loop : -1.73 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 198 TYR 0.016 0.001 TYR B 571 PHE 0.022 0.001 PHE C 89 TRP 0.009 0.001 TRP A 461 HIS 0.004 0.000 HIS B 531 Details of bonding type rmsd covalent geometry : bond 0.00304 (11106) covalent geometry : angle 0.53280 (15041) SS BOND : bond 0.00299 ( 3) SS BOND : angle 0.28029 ( 6) hydrogen bonds : bond 0.03806 ( 599) hydrogen bonds : angle 3.79053 ( 1749) *********************** 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 178 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 130 time to evaluate : 0.417 Fit side-chains REVERT: A 118 ARG cc_start: 0.8271 (mmt90) cc_final: 0.8004 (mmt90) REVERT: A 134 GLN cc_start: 0.7961 (tt0) cc_final: 0.7427 (pt0) REVERT: B 50 ARG cc_start: 0.7722 (ttp-170) cc_final: 0.7462 (ttm110) REVERT: B 116 ASP cc_start: 0.8550 (m-30) cc_final: 0.8287 (m-30) REVERT: B 319 ASP cc_start: 0.8302 (m-30) cc_final: 0.8101 (m-30) REVERT: B 477 MET cc_start: 0.9153 (ttp) cc_final: 0.8917 (ttp) REVERT: C 32 GLN cc_start: 0.8910 (mp10) cc_final: 0.8695 (mp10) REVERT: C 101 TYR cc_start: 0.8978 (m-80) cc_final: 0.8367 (m-80) REVERT: D 99 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7260 (mp0) outliers start: 48 outliers final: 37 residues processed: 168 average time/residue: 0.1118 time to fit residues: 26.5510 Evaluate side-chains 165 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 207 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 276 THR 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 32 SER 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 428 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 560 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 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 46 SER Chi-restraints excluded: chain D residue 87 SER 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: 0.9990 chunk 60 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 73 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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** D 57 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.107514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.080332 restraints weight = 15682.234| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.23 r_work: 0.2717 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11109 Z= 0.190 Angle : 0.573 11.909 15047 Z= 0.287 Chirality : 0.042 0.179 1716 Planarity : 0.004 0.037 1884 Dihedral : 4.947 49.401 1637 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.90 % Allowed : 16.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.24), residues: 1351 helix: 1.83 (0.20), residues: 700 sheet: -0.62 (0.36), residues: 197 loop : -1.72 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 550 TYR 0.017 0.001 TYR B 571 PHE 0.017 0.001 PHE B 595 TRP 0.010 0.001 TRP B 584 HIS 0.004 0.001 HIS B 531 Details of bonding type rmsd covalent geometry : bond 0.00462 (11106) covalent geometry : angle 0.57278 (15041) SS BOND : bond 0.00352 ( 3) SS BOND : angle 0.34744 ( 6) hydrogen bonds : bond 0.04379 ( 599) hydrogen bonds : angle 3.89598 ( 1749) *********************** 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 186 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 128 time to evaluate : 0.458 Fit side-chains REVERT: A 118 ARG cc_start: 0.8271 (mmt90) cc_final: 0.7945 (mmt90) REVERT: A 134 GLN cc_start: 0.8075 (tt0) cc_final: 0.7499 (pt0) REVERT: B 50 ARG cc_start: 0.7747 (ttp-170) cc_final: 0.7450 (ttm110) REVERT: B 116 ASP cc_start: 0.8549 (m-30) cc_final: 0.8301 (m-30) REVERT: C 32 GLN cc_start: 0.8952 (mp10) cc_final: 0.8737 (mp10) REVERT: C 86 LYS cc_start: 0.8733 (tttp) cc_final: 0.8241 (ttmt) REVERT: C 101 TYR cc_start: 0.8994 (m-80) cc_final: 0.8501 (m-80) REVERT: D 99 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7269 (mp0) outliers start: 58 outliers final: 46 residues processed: 173 average time/residue: 0.1044 time to fit residues: 26.0865 Evaluate side-chains 170 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 123 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 172 MET 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 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 444 SER Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 560 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 38 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3280 r_free = 0.3280 target = 0.108232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.081076 restraints weight = 15700.784| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.21 r_work: 0.2729 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11109 Z= 0.157 Angle : 0.560 13.687 15047 Z= 0.278 Chirality : 0.041 0.193 1716 Planarity : 0.003 0.034 1884 Dihedral : 4.929 51.637 1637 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.90 % Allowed : 16.30 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.24), residues: 1351 helix: 1.93 (0.20), residues: 701 sheet: -0.55 (0.37), residues: 197 loop : -1.63 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 26 TYR 0.016 0.001 TYR B 571 PHE 0.030 0.001 PHE C 89 TRP 0.010 0.001 TRP B 584 HIS 0.004 0.001 HIS B 531 Details of bonding type rmsd covalent geometry : bond 0.00376 (11106) covalent geometry : angle 0.55975 (15041) SS BOND : bond 0.00211 ( 3) SS BOND : angle 0.28668 ( 6) hydrogen bonds : bond 0.04101 ( 599) hydrogen bonds : angle 3.86364 ( 1749) *********************** 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 184 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 126 time to evaluate : 0.425 Fit side-chains REVERT: A 118 ARG cc_start: 0.8258 (mmt90) cc_final: 0.7921 (mmt90) REVERT: A 134 GLN cc_start: 0.8025 (tt0) cc_final: 0.7494 (pt0) REVERT: A 302 MET cc_start: 0.8660 (tpp) cc_final: 0.8442 (mmm) REVERT: A 313 GLU cc_start: 0.7851 (tp30) cc_final: 0.7587 (tm-30) REVERT: B 50 ARG cc_start: 0.7739 (ttp-170) cc_final: 0.7454 (ttm110) REVERT: B 116 ASP cc_start: 0.8564 (m-30) cc_final: 0.8305 (m-30) REVERT: C 32 GLN cc_start: 0.8954 (mp10) cc_final: 0.8734 (mp10) REVERT: C 53 MET cc_start: 0.8967 (mmm) cc_final: 0.8732 (mmm) REVERT: C 86 LYS cc_start: 0.8717 (tttp) cc_final: 0.8250 (ttmt) REVERT: C 101 TYR cc_start: 0.9001 (m-80) cc_final: 0.8496 (m-80) REVERT: D 37 GLU cc_start: 0.8479 (pm20) cc_final: 0.8224 (pm20) REVERT: D 99 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7286 (mp0) outliers start: 58 outliers final: 46 residues processed: 172 average time/residue: 0.1036 time to fit residues: 25.5120 Evaluate side-chains 168 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 121 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 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 214 SER 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 444 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 560 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 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 83 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 59 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 86 optimal weight: 0.2980 chunk 76 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3283 r_free = 0.3283 target = 0.108463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.081715 restraints weight = 15722.418| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.17 r_work: 0.2743 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11109 Z= 0.145 Angle : 0.566 13.161 15047 Z= 0.279 Chirality : 0.041 0.200 1716 Planarity : 0.003 0.033 1884 Dihedral : 4.923 53.751 1637 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.73 % Allowed : 16.47 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.24), residues: 1351 helix: 2.00 (0.20), residues: 701 sheet: -0.50 (0.37), residues: 186 loop : -1.58 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 26 TYR 0.016 0.001 TYR B 571 PHE 0.019 0.001 PHE C 89 TRP 0.010 0.001 TRP A 461 HIS 0.004 0.001 HIS B 531 Details of bonding type rmsd covalent geometry : bond 0.00346 (11106) covalent geometry : angle 0.56568 (15041) SS BOND : bond 0.00198 ( 3) SS BOND : angle 0.26156 ( 6) hydrogen bonds : bond 0.03994 ( 599) hydrogen bonds : angle 3.82836 ( 1749) *********************** 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 180 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 124 time to evaluate : 0.381 Fit side-chains REVERT: A 108 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8409 (p) REVERT: A 118 ARG cc_start: 0.8164 (mmt90) cc_final: 0.7799 (mmt90) REVERT: A 134 GLN cc_start: 0.8001 (tt0) cc_final: 0.7481 (pt0) REVERT: A 302 MET cc_start: 0.8707 (tpp) cc_final: 0.8456 (mmm) REVERT: A 313 GLU cc_start: 0.7851 (tp30) cc_final: 0.7570 (tm-30) REVERT: B 116 ASP cc_start: 0.8526 (m-30) cc_final: 0.8249 (m-30) REVERT: B 208 MET cc_start: 0.7051 (pp-130) cc_final: 0.6765 (ppp) REVERT: C 32 GLN cc_start: 0.8957 (mp10) cc_final: 0.8732 (mp10) REVERT: C 53 MET cc_start: 0.8992 (mmm) cc_final: 0.8762 (mmm) REVERT: C 86 LYS cc_start: 0.8688 (tttp) cc_final: 0.8205 (ttmt) REVERT: C 101 TYR cc_start: 0.8967 (m-80) cc_final: 0.8424 (m-80) REVERT: D 37 GLU cc_start: 0.8472 (pm20) cc_final: 0.8227 (pm20) REVERT: D 99 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7219 (mp0) outliers start: 56 outliers final: 49 residues processed: 169 average time/residue: 0.1097 time to fit residues: 26.4782 Evaluate side-chains 172 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 121 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 126 GLN 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 214 SER 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 290 THR 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 444 SER Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 560 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 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 83 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 132 optimal weight: 4.9990 chunk 57 optimal weight: 0.0010 chunk 122 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- 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 = 0.3295 r_free = 0.3295 target = 0.109280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.082268 restraints weight = 15602.587| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.21 r_work: 0.2743 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.2902 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= 0.125 Angle : 0.552 13.813 15047 Z= 0.272 Chirality : 0.040 0.193 1716 Planarity : 0.003 0.033 1884 Dihedral : 4.892 56.051 1637 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.22 % Allowed : 16.89 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.24), residues: 1351 helix: 2.08 (0.20), residues: 700 sheet: -0.49 (0.37), residues: 186 loop : -1.50 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 26 TYR 0.016 0.001 TYR B 571 PHE 0.014 0.001 PHE B 595 TRP 0.010 0.001 TRP A 461 HIS 0.005 0.000 HIS B 531 Details of bonding type rmsd covalent geometry : bond 0.00292 (11106) covalent geometry : angle 0.55192 (15041) SS BOND : bond 0.00218 ( 3) SS BOND : angle 0.27923 ( 6) hydrogen bonds : bond 0.03826 ( 599) hydrogen bonds : angle 3.82434 ( 1749) *********************** 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 174 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 124 time to evaluate : 0.434 Fit side-chains REVERT: A 108 THR cc_start: 0.8648 (OUTLIER) cc_final: 0.8428 (p) REVERT: A 118 ARG cc_start: 0.8189 (mmt90) cc_final: 0.7927 (mmt90) REVERT: A 134 GLN cc_start: 0.7968 (tt0) cc_final: 0.7469 (pt0) REVERT: A 302 MET cc_start: 0.8712 (tpp) cc_final: 0.8503 (mmm) REVERT: A 313 GLU cc_start: 0.7869 (tp30) cc_final: 0.7581 (tm-30) REVERT: B 116 ASP cc_start: 0.8570 (m-30) cc_final: 0.8297 (m-30) REVERT: B 208 MET cc_start: 0.7025 (pp-130) cc_final: 0.6733 (ppp) REVERT: C 32 GLN cc_start: 0.8942 (mp10) cc_final: 0.8724 (mp10) REVERT: C 39 LEU cc_start: 0.8956 (mp) cc_final: 0.8585 (mp) REVERT: C 86 LYS cc_start: 0.8658 (tttp) cc_final: 0.8224 (ttmt) REVERT: C 101 TYR cc_start: 0.8990 (m-80) cc_final: 0.8459 (m-80) REVERT: D 99 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7289 (mp0) outliers start: 50 outliers final: 45 residues processed: 164 average time/residue: 0.1123 time to fit residues: 26.0941 Evaluate side-chains 167 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 120 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 108 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 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 214 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 290 THR 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 560 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 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 83 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.8091 > 50: distance: 9 - 15: 21.149 distance: 15 - 16: 35.897 distance: 15 - 21: 37.203 distance: 16 - 17: 5.769 distance: 17 - 18: 52.283 distance: 17 - 22: 57.234 distance: 19 - 20: 40.205 distance: 20 - 21: 39.757 distance: 22 - 23: 13.840 distance: 23 - 24: 44.239 distance: 23 - 26: 34.400 distance: 24 - 25: 49.559 distance: 24 - 30: 13.070 distance: 26 - 27: 32.586 distance: 27 - 28: 38.307 distance: 27 - 29: 19.632 distance: 30 - 31: 38.608 distance: 31 - 34: 41.443 distance: 32 - 33: 39.797 distance: 32 - 37: 38.957 distance: 34 - 35: 40.335 distance: 34 - 36: 70.116 distance: 37 - 38: 56.457 distance: 38 - 39: 56.773 distance: 38 - 41: 9.351 distance: 39 - 40: 68.473 distance: 39 - 45: 41.439 distance: 41 - 42: 18.746 distance: 42 - 43: 23.993 distance: 42 - 44: 44.041 distance: 45 - 46: 60.763 distance: 45 - 216: 28.598 distance: 46 - 47: 67.096 distance: 46 - 49: 39.624 distance: 47 - 48: 51.584 distance: 47 - 54: 40.947 distance: 48 - 213: 36.432 distance: 49 - 50: 43.117 distance: 50 - 51: 33.903 distance: 51 - 52: 16.346 distance: 51 - 53: 32.138 distance: 54 - 55: 57.985 distance: 55 - 56: 66.043 distance: 55 - 58: 42.412 distance: 56 - 57: 53.980 distance: 56 - 61: 60.191 distance: 58 - 59: 48.683 distance: 58 - 60: 26.279 distance: 61 - 62: 28.480 distance: 61 - 200: 26.316 distance: 62 - 63: 31.396 distance: 62 - 65: 24.143 distance: 63 - 64: 34.448 distance: 63 - 72: 44.997 distance: 64 - 197: 32.304 distance: 65 - 66: 29.444 distance: 66 - 67: 28.724 distance: 67 - 68: 23.035 distance: 68 - 69: 14.853 distance: 69 - 70: 14.246 distance: 69 - 71: 14.687 distance: 72 - 73: 4.666 distance: 73 - 74: 54.579 distance: 73 - 76: 3.032 distance: 74 - 75: 38.936 distance: 76 - 77: 43.032 distance: 77 - 78: 38.075 distance: 77 - 79: 54.779 distance: 80 - 81: 42.026 distance: 80 - 125: 35.889 distance: 81 - 82: 57.701 distance: 81 - 84: 42.983 distance: 82 - 83: 39.998 distance: 83 - 122: 36.646 distance: 84 - 85: 39.916 distance: 85 - 86: 41.348 distance: 85 - 87: 42.072 distance: 88 - 89: 6.308 distance: 89 - 90: 7.942 distance: 89 - 92: 31.563 distance: 90 - 91: 56.803 distance: 90 - 96: 33.809 distance: 92 - 93: 54.315 distance: 93 - 94: 6.668 distance: 93 - 95: 46.479