Starting phenix.real_space_refine on Wed Feb 4 20:31:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jor_61683/02_2026/9jor_61683.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jor_61683/02_2026/9jor_61683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jor_61683/02_2026/9jor_61683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jor_61683/02_2026/9jor_61683.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jor_61683/02_2026/9jor_61683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jor_61683/02_2026/9jor_61683.map" } resolution = 3.09 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= -0.000 sd= 0.047 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: 6 Type Number sf(0) Gaussians P 48 5.49 5 Mg 3 5.21 5 S 44 5.16 5 C 7953 2.51 5 N 2157 2.21 5 O 2492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 12697 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3563 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 13, 'TRANS': 428} Chain: "A" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2292 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 7, 'TRANS': 276} Chain: "D" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3563 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 13, 'TRANS': 428} Chain: "B" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2292 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 7, 'TRANS': 276} Chain: "E" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 493 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "F" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 491 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.55, per 1000 atoms: 0.20 Number of scatterers: 12697 At special positions: 0 Unit cell: (117.52, 127.92, 115.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 44 16.00 P 48 15.00 Mg 3 11.99 O 2492 8.00 N 2157 7.00 C 7953 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 436.7 milliseconds 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2716 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 22 sheets defined 43.9% alpha, 11.0% beta 17 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'C' and resid 8 through 26 removed outlier: 3.504A pdb=" N ALA C 16 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU C 17 " --> pdb=" O ASP C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 52 Processing helix chain 'C' and resid 61 through 65 Processing helix chain 'C' and resid 67 through 72 removed outlier: 4.147A pdb=" N LEU C 71 " --> pdb=" O GLY C 67 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY C 72 " --> pdb=" O VAL C 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 67 through 72' Processing helix chain 'C' and resid 76 through 86 removed outlier: 4.042A pdb=" N ALA C 80 " --> pdb=" O GLY C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 129 removed outlier: 3.627A pdb=" N TYR C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 161 removed outlier: 3.873A pdb=" N ASN C 160 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY C 161 " --> pdb=" O VAL C 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 156 through 161' Processing helix chain 'C' and resid 177 through 191 Processing helix chain 'C' and resid 240 through 254 removed outlier: 3.797A pdb=" N LYS C 246 " --> pdb=" O THR C 242 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ASP C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Proline residue: C 250 - end of helix Processing helix chain 'C' and resid 283 through 295 Processing helix chain 'C' and resid 323 through 365 removed outlier: 4.730A pdb=" N GLU C 329 " --> pdb=" O LYS C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 381 Processing helix chain 'C' and resid 391 through 397 Processing helix chain 'C' and resid 404 through 427 removed outlier: 4.035A pdb=" N LYS C 409 " --> pdb=" O SER C 405 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS C 410 " --> pdb=" O ASP C 406 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 440 removed outlier: 3.632A pdb=" N GLU C 439 " --> pdb=" O THR C 435 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU C 440 " --> pdb=" O LYS C 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 420 Processing helix chain 'A' and resid 422 through 427 Processing helix chain 'A' and resid 451 through 454 Processing helix chain 'A' and resid 455 through 466 removed outlier: 5.147A pdb=" N ILE A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 515 Processing helix chain 'A' and resid 523 through 527 Processing helix chain 'A' and resid 528 through 535 Processing helix chain 'A' and resid 559 through 565 Processing helix chain 'A' and resid 566 through 575 Processing helix chain 'A' and resid 607 through 612 Processing helix chain 'A' and resid 613 through 618 removed outlier: 5.989A pdb=" N ASP A 616 " --> pdb=" O SER A 613 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU A 618 " --> pdb=" O LYS A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 643 Processing helix chain 'A' and resid 654 through 663 Processing helix chain 'A' and resid 667 through 675 Processing helix chain 'D' and resid 8 through 26 removed outlier: 3.697A pdb=" N ALA D 16 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU D 17 " --> pdb=" O ASP D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 51 Processing helix chain 'D' and resid 61 through 65 Processing helix chain 'D' and resid 76 through 87 removed outlier: 3.793A pdb=" N ALA D 80 " --> pdb=" O GLY D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 130 removed outlier: 3.615A pdb=" N TYR D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 161 removed outlier: 3.668A pdb=" N ASN D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY D 161 " --> pdb=" O VAL D 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 156 through 161' Processing helix chain 'D' and resid 177 through 191 removed outlier: 3.529A pdb=" N LYS D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 245 Processing helix chain 'D' and resid 248 through 253 removed outlier: 3.607A pdb=" N ASN D 253 " --> pdb=" O ASP D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 295 Processing helix chain 'D' and resid 319 through 365 removed outlier: 3.625A pdb=" N LEU D 323 " --> pdb=" O ASN D 319 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR D 333 " --> pdb=" O GLU D 329 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR D 334 " --> pdb=" O VAL D 330 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER D 365 " --> pdb=" O LYS D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 385 Processing helix chain 'D' and resid 388 through 391 Processing helix chain 'D' and resid 392 through 398 removed outlier: 4.074A pdb=" N VAL D 396 " --> pdb=" O VAL D 392 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 403 Processing helix chain 'D' and resid 407 through 428 Processing helix chain 'D' and resid 429 through 439 Processing helix chain 'B' and resid 416 through 420 Processing helix chain 'B' and resid 423 through 427 removed outlier: 3.823A pdb=" N ARG B 427 " --> pdb=" O ILE B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 455 through 466 Processing helix chain 'B' and resid 509 through 515 Processing helix chain 'B' and resid 523 through 527 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 559 through 565 Processing helix chain 'B' and resid 566 through 575 removed outlier: 4.427A pdb=" N GLY B 572 " --> pdb=" O PRO B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 583 removed outlier: 4.043A pdb=" N PHE B 581 " --> pdb=" O TRP B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 613 Processing helix chain 'B' and resid 628 through 632 removed outlier: 3.685A pdb=" N LEU B 632 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 643 Processing helix chain 'B' and resid 654 through 664 Processing helix chain 'B' and resid 666 through 675 removed outlier: 3.934A pdb=" N ARG B 670 " --> pdb=" O ASN B 666 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 59 through 60 Processing sheet with id=AA3, first strand: chain 'C' and resid 130 through 131 removed outlier: 4.117A pdb=" N LEU C 151 " --> pdb=" O LYS C 131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 162 through 165 Processing sheet with id=AA5, first strand: chain 'C' and resid 207 through 211 removed outlier: 3.842A pdb=" N ILE C 211 " --> pdb=" O GLN C 214 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 221 through 223 Processing sheet with id=AA7, first strand: chain 'C' and resid 306 through 308 Processing sheet with id=AA8, first strand: chain 'A' and resid 474 through 476 Processing sheet with id=AA9, first strand: chain 'A' and resid 490 through 495 removed outlier: 4.247A pdb=" N TRP A 482 " --> pdb=" O ILE A 522 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 505 through 508 Processing sheet with id=AB2, first strand: chain 'A' and resid 603 through 605 Processing sheet with id=AB3, first strand: chain 'D' and resid 2 through 7 removed outlier: 3.684A pdb=" N ASN D 4 " --> pdb=" O TYR B 646 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 59 through 60 Processing sheet with id=AB5, first strand: chain 'D' and resid 162 through 165 Processing sheet with id=AB6, first strand: chain 'D' and resid 214 through 218 Processing sheet with id=AB7, first strand: chain 'D' and resid 228 through 230 Processing sheet with id=AB8, first strand: chain 'D' and resid 306 through 308 Processing sheet with id=AB9, first strand: chain 'B' and resid 435 through 436 removed outlier: 6.308A pdb=" N PHE B 412 " --> pdb=" O TYR B 435 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU B 411 " --> pdb=" O ALA B 553 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 474 through 476 removed outlier: 7.101A pdb=" N GLU B 475 " --> pdb=" O LYS B 543 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 490 through 495 removed outlier: 3.990A pdb=" N TRP B 482 " --> pdb=" O ILE B 522 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 505 through 508 Processing sheet with id=AC4, first strand: chain 'B' and resid 594 through 598 463 hydrogen bonds defined for protein. 1284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 1.73 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2220 1.32 - 1.44: 3531 1.44 - 1.57: 7125 1.57 - 1.69: 94 1.69 - 1.81: 82 Bond restraints: 13052 Sorted by residual: bond pdb=" CA MET B 547 " pdb=" C MET B 547 " ideal model delta sigma weight residual 1.523 1.459 0.064 1.30e-02 5.92e+03 2.41e+01 bond pdb=" N MET A 547 " pdb=" CA MET A 547 " ideal model delta sigma weight residual 1.457 1.410 0.047 1.29e-02 6.01e+03 1.34e+01 bond pdb=" CA ASP B 559 " pdb=" C ASP B 559 " ideal model delta sigma weight residual 1.528 1.485 0.043 1.37e-02 5.33e+03 9.88e+00 bond pdb=" N MET B 547 " pdb=" CA MET B 547 " ideal model delta sigma weight residual 1.461 1.422 0.039 1.30e-02 5.92e+03 9.11e+00 bond pdb=" CA HIS B 560 " pdb=" C HIS B 560 " ideal model delta sigma weight residual 1.523 1.486 0.037 1.30e-02 5.92e+03 8.20e+00 ... (remaining 13047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 17649 2.56 - 5.12: 121 5.12 - 7.68: 13 7.68 - 10.24: 5 10.24 - 12.80: 2 Bond angle restraints: 17790 Sorted by residual: angle pdb=" CA PRO B 619 " pdb=" N PRO B 619 " pdb=" CD PRO B 619 " ideal model delta sigma weight residual 112.00 102.88 9.12 1.40e+00 5.10e-01 4.24e+01 angle pdb=" N PRO B 619 " pdb=" CD PRO B 619 " pdb=" CG PRO B 619 " ideal model delta sigma weight residual 103.20 94.34 8.86 1.50e+00 4.44e-01 3.49e+01 angle pdb=" N LYS B 543 " pdb=" CA LYS B 543 " pdb=" C LYS B 543 " ideal model delta sigma weight residual 111.40 105.23 6.17 1.22e+00 6.72e-01 2.56e+01 angle pdb=" C GLU B 475 " pdb=" N GLU B 476 " pdb=" CA GLU B 476 " ideal model delta sigma weight residual 122.74 113.65 9.09 1.82e+00 3.02e-01 2.49e+01 angle pdb=" N SER B 546 " pdb=" CA SER B 546 " pdb=" C SER B 546 " ideal model delta sigma weight residual 114.12 107.31 6.81 1.39e+00 5.18e-01 2.40e+01 ... (remaining 17785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.03: 7109 30.03 - 60.06: 618 60.06 - 90.09: 37 90.09 - 120.13: 0 120.13 - 150.16: 2 Dihedral angle restraints: 7766 sinusoidal: 3536 harmonic: 4230 Sorted by residual: dihedral pdb=" CA THR D 242 " pdb=" C THR D 242 " pdb=" N TYR D 243 " pdb=" CA TYR D 243 " ideal model delta harmonic sigma weight residual 180.00 155.05 24.95 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA PHE C 36 " pdb=" C PHE C 36 " pdb=" N LYS C 37 " pdb=" CA LYS C 37 " ideal model delta harmonic sigma weight residual 180.00 157.47 22.53 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA VAL C 321 " pdb=" C VAL C 321 " pdb=" N ASP C 322 " pdb=" CA ASP C 322 " ideal model delta harmonic sigma weight residual 180.00 158.46 21.54 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 7763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1454 0.042 - 0.084: 374 0.084 - 0.126: 91 0.126 - 0.168: 6 0.168 - 0.210: 3 Chirality restraints: 1928 Sorted by residual: chirality pdb=" CB ILE C 165 " pdb=" CA ILE C 165 " pdb=" CG1 ILE C 165 " pdb=" CG2 ILE C 165 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ALA B 558 " pdb=" N ALA B 558 " pdb=" C ALA B 558 " pdb=" CB ALA B 558 " both_signs ideal model delta sigma weight residual False 2.48 2.30 0.19 2.00e-01 2.50e+01 8.58e-01 chirality pdb=" CA ILE C 165 " pdb=" N ILE C 165 " pdb=" C ILE C 165 " pdb=" CB ILE C 165 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.47e-01 ... (remaining 1925 not shown) Planarity restraints: 2110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 542 " 0.022 2.00e-02 2.50e+03 4.40e-02 1.94e+01 pdb=" C ILE B 542 " -0.076 2.00e-02 2.50e+03 pdb=" O ILE B 542 " 0.029 2.00e-02 2.50e+03 pdb=" N LYS B 543 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 543 " 0.022 2.00e-02 2.50e+03 4.33e-02 1.88e+01 pdb=" C LYS A 543 " -0.075 2.00e-02 2.50e+03 pdb=" O LYS A 543 " 0.028 2.00e-02 2.50e+03 pdb=" N SER A 544 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 470 " 0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C GLY B 470 " -0.056 2.00e-02 2.50e+03 pdb=" O GLY B 470 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU B 471 " 0.019 2.00e-02 2.50e+03 ... (remaining 2107 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 76 2.49 - 3.09: 8659 3.09 - 3.70: 19569 3.70 - 4.30: 29112 4.30 - 4.90: 47899 Nonbonded interactions: 105315 Sorted by model distance: nonbonded pdb=" ND2 ASN D 5 " pdb=" ND2 ASN B 536 " model vdw 1.891 3.200 nonbonded pdb=" OD2 ASP A 557 " pdb="MG MG A 701 " model vdw 2.007 2.170 nonbonded pdb=" O LEU A 431 " pdb=" ND1 HIS A 432 " model vdw 2.055 3.120 nonbonded pdb=" O TRP D 91 " pdb=" OH TYR D 236 " model vdw 2.176 3.040 nonbonded pdb=" O ALA A 550 " pdb=" ND2 ASN A 551 " model vdw 2.201 3.120 ... (remaining 105310 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 393 through 701) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 0.930 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: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.790 Find NCS groups from input model: 0.110 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 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 : 0.004 0.069 13052 Z= 0.196 Angle : 0.604 12.797 17790 Z= 0.344 Chirality : 0.040 0.210 1928 Planarity : 0.004 0.049 2110 Dihedral : 19.649 150.158 5050 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.79 % Allowed : 28.13 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.94 (0.22), residues: 1444 helix: 0.31 (0.23), residues: 554 sheet: -1.91 (0.39), residues: 186 loop : -0.94 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 351 TYR 0.016 0.001 TYR D 334 PHE 0.024 0.001 PHE B 474 TRP 0.011 0.001 TRP A 673 HIS 0.005 0.001 HIS A 397 Details of bonding type rmsd covalent geometry : bond 0.00389 (13052) covalent geometry : angle 0.60420 (17790) hydrogen bonds : bond 0.17552 ( 502) hydrogen bonds : angle 6.69182 ( 1362) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 539 ARG cc_start: 0.4953 (ptt180) cc_final: 0.4706 (ptt180) REVERT: A 582 GLU cc_start: 0.7509 (tt0) cc_final: 0.6794 (tm-30) REVERT: D 252 GLU cc_start: 0.7152 (pp20) cc_final: 0.6650 (tt0) REVERT: D 351 ARG cc_start: 0.7598 (ttm-80) cc_final: 0.6658 (mmp80) REVERT: D 398 MET cc_start: 0.5520 (mmm) cc_final: 0.4571 (mmm) REVERT: B 449 TYR cc_start: 0.8716 (m-10) cc_final: 0.8384 (m-10) REVERT: B 546 SER cc_start: 0.8368 (OUTLIER) cc_final: 0.8078 (t) outliers start: 10 outliers final: 4 residues processed: 162 average time/residue: 0.1029 time to fit residues: 24.0296 Evaluate side-chains 147 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 142 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain B residue 546 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.1980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN C 103 ASN C 303 GLN A 501 GLN D 5 ASN D 93 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.184441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.137783 restraints weight = 16003.139| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.69 r_work: 0.3517 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13052 Z= 0.223 Angle : 0.589 5.822 17790 Z= 0.325 Chirality : 0.042 0.158 1928 Planarity : 0.004 0.055 2110 Dihedral : 16.421 149.892 2133 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.57 % Allowed : 24.88 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.95 (0.22), residues: 1444 helix: 0.42 (0.23), residues: 544 sheet: -2.12 (0.38), residues: 186 loop : -0.97 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 351 TYR 0.016 0.001 TYR D 334 PHE 0.017 0.002 PHE A 581 TRP 0.011 0.001 TRP B 506 HIS 0.004 0.001 HIS C 74 Details of bonding type rmsd covalent geometry : bond 0.00524 (13052) covalent geometry : angle 0.58886 (17790) hydrogen bonds : bond 0.04200 ( 502) hydrogen bonds : angle 5.08357 ( 1362) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 159 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 244 VAL cc_start: 0.8090 (t) cc_final: 0.7866 (t) REVERT: A 431 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7368 (pp) REVERT: A 432 HIS cc_start: 0.8609 (OUTLIER) cc_final: 0.8271 (m90) REVERT: A 551 ASN cc_start: 0.8625 (OUTLIER) cc_final: 0.8189 (m-40) REVERT: A 582 GLU cc_start: 0.7923 (tt0) cc_final: 0.7087 (tm-30) REVERT: D 190 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7052 (mp10) REVERT: D 351 ARG cc_start: 0.7769 (ttm-80) cc_final: 0.6806 (mmp80) REVERT: D 381 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7554 (mm-30) REVERT: D 398 MET cc_start: 0.5677 (mmm) cc_final: 0.4537 (mmm) REVERT: B 449 TYR cc_start: 0.8811 (m-80) cc_final: 0.8461 (m-10) REVERT: B 471 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7157 (tt0) REVERT: B 546 SER cc_start: 0.8525 (OUTLIER) cc_final: 0.8272 (t) REVERT: B 619 PRO cc_start: 0.7295 (Cg_exo) cc_final: 0.7006 (Cg_endo) outliers start: 45 outliers final: 22 residues processed: 194 average time/residue: 0.1152 time to fit residues: 31.8076 Evaluate side-chains 180 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 539 ARG Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 623 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 121 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 131 optimal weight: 0.0970 chunk 96 optimal weight: 0.5980 chunk 132 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 ASN B 576 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.185318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.136727 restraints weight = 16150.927| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.29 r_work: 0.3571 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13052 Z= 0.125 Angle : 0.510 5.610 17790 Z= 0.286 Chirality : 0.039 0.141 1928 Planarity : 0.003 0.052 2110 Dihedral : 16.354 147.893 2125 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.72 % Allowed : 24.96 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.23), residues: 1444 helix: 0.58 (0.23), residues: 558 sheet: -2.09 (0.38), residues: 186 loop : -0.93 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 351 TYR 0.013 0.001 TYR D 117 PHE 0.010 0.001 PHE A 605 TRP 0.008 0.001 TRP B 673 HIS 0.012 0.001 HIS A 621 Details of bonding type rmsd covalent geometry : bond 0.00281 (13052) covalent geometry : angle 0.51026 (17790) hydrogen bonds : bond 0.03326 ( 502) hydrogen bonds : angle 4.69333 ( 1362) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 158 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: C 244 VAL cc_start: 0.8010 (t) cc_final: 0.7799 (t) REVERT: C 324 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8167 (mp) REVERT: A 431 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7371 (pp) REVERT: A 432 HIS cc_start: 0.8404 (OUTLIER) cc_final: 0.7844 (m90) REVERT: A 435 TYR cc_start: 0.8467 (t80) cc_final: 0.8259 (t80) REVERT: A 547 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7602 (mtt) REVERT: A 551 ASN cc_start: 0.8462 (OUTLIER) cc_final: 0.8016 (m-40) REVERT: A 582 GLU cc_start: 0.7886 (tt0) cc_final: 0.6967 (tm-30) REVERT: A 583 GLN cc_start: 0.7149 (OUTLIER) cc_final: 0.6877 (mp10) REVERT: A 605 PHE cc_start: 0.7926 (m-80) cc_final: 0.7541 (m-80) REVERT: A 657 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7555 (tm-30) REVERT: D 187 GLN cc_start: 0.7979 (mt0) cc_final: 0.7708 (mt0) REVERT: D 190 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.6961 (mp10) REVERT: D 196 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7183 (ttmt) REVERT: D 351 ARG cc_start: 0.7830 (ttm-80) cc_final: 0.6790 (mmp80) REVERT: D 381 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7590 (mm-30) REVERT: D 398 MET cc_start: 0.5771 (mmm) cc_final: 0.4806 (mmm) REVERT: B 449 TYR cc_start: 0.8779 (m-80) cc_final: 0.8424 (m-10) REVERT: B 471 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6967 (tt0) REVERT: B 472 LYS cc_start: 0.8140 (ptpt) cc_final: 0.7728 (ttmm) REVERT: B 619 PRO cc_start: 0.7281 (Cg_exo) cc_final: 0.7067 (Cg_endo) outliers start: 47 outliers final: 19 residues processed: 193 average time/residue: 0.0976 time to fit residues: 28.2175 Evaluate side-chains 176 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 583 GLN Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 539 ARG Chi-restraints excluded: chain B residue 613 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 0 optimal weight: 6.9990 chunk 88 optimal weight: 0.0870 chunk 34 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 52 optimal weight: 0.3980 chunk 67 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 80 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 134 optimal weight: 0.8980 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 ASN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.185331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.136934 restraints weight = 16017.865| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.27 r_work: 0.3573 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13052 Z= 0.128 Angle : 0.509 6.403 17790 Z= 0.283 Chirality : 0.039 0.141 1928 Planarity : 0.003 0.052 2110 Dihedral : 16.294 147.267 2124 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.88 % Allowed : 24.64 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.72 (0.22), residues: 1444 helix: 0.72 (0.23), residues: 548 sheet: -2.05 (0.38), residues: 186 loop : -0.93 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 351 TYR 0.013 0.001 TYR D 334 PHE 0.012 0.001 PHE A 581 TRP 0.012 0.001 TRP D 91 HIS 0.012 0.001 HIS A 621 Details of bonding type rmsd covalent geometry : bond 0.00295 (13052) covalent geometry : angle 0.50916 (17790) hydrogen bonds : bond 0.03132 ( 502) hydrogen bonds : angle 4.50393 ( 1362) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 155 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: C 324 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8232 (mp) REVERT: A 431 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7333 (pp) REVERT: A 432 HIS cc_start: 0.8380 (OUTLIER) cc_final: 0.7874 (m90) REVERT: A 452 MET cc_start: 0.8140 (mtt) cc_final: 0.7659 (mtm) REVERT: A 547 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7542 (mtt) REVERT: A 551 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.8018 (m-40) REVERT: A 582 GLU cc_start: 0.7912 (tt0) cc_final: 0.6977 (tm-30) REVERT: A 583 GLN cc_start: 0.7194 (OUTLIER) cc_final: 0.6908 (mp10) REVERT: D 49 ASP cc_start: 0.7743 (t0) cc_final: 0.7525 (m-30) REVERT: D 190 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.6746 (mp10) REVERT: D 196 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7138 (ttmt) REVERT: D 381 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7586 (mm-30) REVERT: D 398 MET cc_start: 0.5777 (mmm) cc_final: 0.4898 (mmm) REVERT: D 426 LYS cc_start: 0.8424 (mmmt) cc_final: 0.7843 (mttt) REVERT: B 449 TYR cc_start: 0.8784 (m-10) cc_final: 0.8439 (m-10) REVERT: B 471 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6937 (tt0) REVERT: B 472 LYS cc_start: 0.8158 (ptpt) cc_final: 0.7700 (mtpp) REVERT: B 619 PRO cc_start: 0.7314 (Cg_exo) cc_final: 0.7095 (Cg_endo) outliers start: 49 outliers final: 29 residues processed: 194 average time/residue: 0.1076 time to fit residues: 30.6166 Evaluate side-chains 187 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 581 PHE Chi-restraints excluded: chain A residue 583 GLN Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 539 ARG Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 623 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 128 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 108 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 86 optimal weight: 0.0030 chunk 20 optimal weight: 1.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 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 = 0.4140 r_free = 0.4140 target = 0.180815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.132242 restraints weight = 16113.608| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.26 r_work: 0.3517 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13052 Z= 0.197 Angle : 0.559 6.253 17790 Z= 0.308 Chirality : 0.041 0.150 1928 Planarity : 0.004 0.053 2110 Dihedral : 16.363 148.511 2124 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 4.36 % Allowed : 24.72 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.83 (0.22), residues: 1444 helix: 0.61 (0.23), residues: 548 sheet: -2.06 (0.38), residues: 186 loop : -1.00 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 351 TYR 0.013 0.001 TYR D 117 PHE 0.016 0.001 PHE A 581 TRP 0.012 0.001 TRP B 673 HIS 0.011 0.001 HIS A 621 Details of bonding type rmsd covalent geometry : bond 0.00465 (13052) covalent geometry : angle 0.55906 (17790) hydrogen bonds : bond 0.03573 ( 502) hydrogen bonds : angle 4.54205 ( 1362) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 161 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 324 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8164 (mp) REVERT: A 431 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.7351 (pp) REVERT: A 432 HIS cc_start: 0.8491 (OUTLIER) cc_final: 0.7924 (m90) REVERT: A 478 GLU cc_start: 0.7642 (pm20) cc_final: 0.7380 (pm20) REVERT: A 547 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7603 (mtt) REVERT: A 549 TYR cc_start: 0.8457 (m-80) cc_final: 0.8021 (m-80) REVERT: A 551 ASN cc_start: 0.8522 (OUTLIER) cc_final: 0.8064 (m-40) REVERT: A 582 GLU cc_start: 0.7892 (tt0) cc_final: 0.6939 (tm-30) REVERT: A 657 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7655 (tm-30) REVERT: D 128 ASN cc_start: 0.8471 (m-40) cc_final: 0.8198 (m110) REVERT: D 190 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.6809 (mp10) REVERT: D 196 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7209 (ttmt) REVERT: D 381 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7582 (mm-30) REVERT: D 398 MET cc_start: 0.5737 (mmm) cc_final: 0.4640 (mmm) REVERT: D 426 LYS cc_start: 0.8478 (mmmt) cc_final: 0.7862 (mttt) REVERT: B 449 TYR cc_start: 0.8875 (m-80) cc_final: 0.8522 (m-10) REVERT: B 472 LYS cc_start: 0.8242 (ptpt) cc_final: 0.7722 (mtpp) outliers start: 55 outliers final: 37 residues processed: 204 average time/residue: 0.1026 time to fit residues: 30.6635 Evaluate side-chains 192 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 147 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 581 PHE Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 623 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 2 optimal weight: 0.2980 chunk 79 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 124 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 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 = 0.4180 r_free = 0.4180 target = 0.184781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.136774 restraints weight = 15881.435| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.26 r_work: 0.3574 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13052 Z= 0.122 Angle : 0.510 8.728 17790 Z= 0.282 Chirality : 0.039 0.167 1928 Planarity : 0.003 0.051 2110 Dihedral : 16.328 146.834 2124 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 4.36 % Allowed : 24.41 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.62 (0.23), residues: 1444 helix: 0.80 (0.23), residues: 548 sheet: -2.22 (0.40), residues: 166 loop : -0.85 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 287 TYR 0.014 0.001 TYR D 334 PHE 0.011 0.001 PHE A 605 TRP 0.009 0.001 TRP B 673 HIS 0.010 0.001 HIS A 621 Details of bonding type rmsd covalent geometry : bond 0.00278 (13052) covalent geometry : angle 0.50990 (17790) hydrogen bonds : bond 0.02960 ( 502) hydrogen bonds : angle 4.35469 ( 1362) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 155 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 ASP cc_start: 0.8490 (m-30) cc_final: 0.8192 (t70) REVERT: C 244 VAL cc_start: 0.7985 (t) cc_final: 0.7770 (t) REVERT: C 324 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8126 (mp) REVERT: A 431 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7264 (pp) REVERT: A 432 HIS cc_start: 0.8386 (OUTLIER) cc_final: 0.7841 (m90) REVERT: A 452 MET cc_start: 0.7963 (mtt) cc_final: 0.7744 (mtt) REVERT: A 475 GLU cc_start: 0.6377 (mm-30) cc_final: 0.6057 (mm-30) REVERT: A 547 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7510 (mtt) REVERT: A 551 ASN cc_start: 0.8275 (OUTLIER) cc_final: 0.7859 (m-40) REVERT: A 582 GLU cc_start: 0.7859 (tt0) cc_final: 0.7114 (tm-30) REVERT: A 657 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7602 (tm-30) REVERT: D 128 ASN cc_start: 0.8458 (m-40) cc_final: 0.8174 (m110) REVERT: D 190 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.6889 (mp10) REVERT: D 196 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7129 (ttmt) REVERT: D 351 ARG cc_start: 0.7926 (ttm-80) cc_final: 0.7329 (tpp-160) REVERT: D 381 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7592 (mm-30) REVERT: D 398 MET cc_start: 0.5769 (mmm) cc_final: 0.4682 (mmm) REVERT: B 449 TYR cc_start: 0.8784 (m-10) cc_final: 0.8400 (m-10) REVERT: B 472 LYS cc_start: 0.8216 (ptpt) cc_final: 0.7731 (mtpp) REVERT: B 612 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8232 (mm-30) REVERT: B 619 PRO cc_start: 0.7349 (Cg_exo) cc_final: 0.7131 (Cg_endo) REVERT: B 624 ARG cc_start: 0.7800 (ttp80) cc_final: 0.7082 (ttt180) outliers start: 55 outliers final: 37 residues processed: 198 average time/residue: 0.1119 time to fit residues: 32.4655 Evaluate side-chains 194 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 149 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 581 PHE Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 539 ARG Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 623 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 19 optimal weight: 0.0980 chunk 95 optimal weight: 0.8980 chunk 139 optimal weight: 0.7980 chunk 41 optimal weight: 0.0970 chunk 3 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 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 = 0.4199 r_free = 0.4199 target = 0.186697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.139036 restraints weight = 15946.325| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.26 r_work: 0.3602 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 13052 Z= 0.110 Angle : 0.498 7.535 17790 Z= 0.277 Chirality : 0.038 0.153 1928 Planarity : 0.003 0.049 2110 Dihedral : 16.289 145.696 2124 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.88 % Allowed : 25.36 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.46 (0.23), residues: 1444 helix: 0.94 (0.23), residues: 548 sheet: -2.14 (0.41), residues: 166 loop : -0.76 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 287 TYR 0.009 0.001 TYR B 435 PHE 0.018 0.001 PHE D 350 TRP 0.011 0.001 TRP D 91 HIS 0.010 0.001 HIS A 621 Details of bonding type rmsd covalent geometry : bond 0.00251 (13052) covalent geometry : angle 0.49813 (17790) hydrogen bonds : bond 0.02770 ( 502) hydrogen bonds : angle 4.20747 ( 1362) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 159 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 ASP cc_start: 0.8527 (m-30) cc_final: 0.8209 (t70) REVERT: C 179 SER cc_start: 0.8859 (OUTLIER) cc_final: 0.8654 (t) REVERT: C 244 VAL cc_start: 0.7983 (t) cc_final: 0.7744 (t) REVERT: C 258 THR cc_start: 0.8310 (m) cc_final: 0.7761 (p) REVERT: C 286 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7698 (tm-30) REVERT: C 322 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7976 (t0) REVERT: A 431 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7380 (pp) REVERT: A 475 GLU cc_start: 0.6497 (mm-30) cc_final: 0.6191 (mm-30) REVERT: A 547 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.7363 (mtt) REVERT: A 551 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.7963 (m-40) REVERT: A 582 GLU cc_start: 0.7863 (tt0) cc_final: 0.7016 (tm-30) REVERT: A 657 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7620 (tm-30) REVERT: D 49 ASP cc_start: 0.7784 (t0) cc_final: 0.7506 (m-30) REVERT: D 128 ASN cc_start: 0.8403 (m-40) cc_final: 0.8136 (m-40) REVERT: D 190 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.6688 (mp10) REVERT: D 196 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7164 (ttmt) REVERT: D 351 ARG cc_start: 0.7908 (ttm-80) cc_final: 0.7365 (tpp-160) REVERT: D 398 MET cc_start: 0.5656 (mmm) cc_final: 0.4578 (mmm) REVERT: D 426 LYS cc_start: 0.8397 (mmmt) cc_final: 0.8136 (mmmt) REVERT: B 449 TYR cc_start: 0.8760 (m-10) cc_final: 0.8383 (m-10) REVERT: B 472 LYS cc_start: 0.8207 (ptpt) cc_final: 0.7736 (mtpp) REVERT: B 612 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8243 (mm-30) REVERT: B 624 ARG cc_start: 0.7802 (ttp80) cc_final: 0.7131 (ttt180) outliers start: 49 outliers final: 33 residues processed: 198 average time/residue: 0.1005 time to fit residues: 29.2212 Evaluate side-chains 191 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 623 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 127 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 139 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.179645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.130913 restraints weight = 15995.770| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.26 r_work: 0.3503 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13052 Z= 0.222 Angle : 0.589 7.727 17790 Z= 0.321 Chirality : 0.042 0.157 1928 Planarity : 0.004 0.053 2110 Dihedral : 16.445 148.541 2124 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 4.12 % Allowed : 25.67 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.22), residues: 1444 helix: 0.70 (0.23), residues: 548 sheet: -2.24 (0.41), residues: 166 loop : -0.88 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 46 TYR 0.016 0.002 TYR C 334 PHE 0.020 0.002 PHE A 581 TRP 0.013 0.001 TRP A 673 HIS 0.009 0.001 HIS A 621 Details of bonding type rmsd covalent geometry : bond 0.00523 (13052) covalent geometry : angle 0.58875 (17790) hydrogen bonds : bond 0.03678 ( 502) hydrogen bonds : angle 4.49079 ( 1362) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 154 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 258 THR cc_start: 0.8370 (m) cc_final: 0.7835 (p) REVERT: C 286 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7707 (tm-30) REVERT: C 324 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8199 (mp) REVERT: A 431 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7382 (pp) REVERT: A 432 HIS cc_start: 0.8597 (OUTLIER) cc_final: 0.8211 (m90) REVERT: A 475 GLU cc_start: 0.6422 (mm-30) cc_final: 0.6151 (mm-30) REVERT: A 549 TYR cc_start: 0.8511 (m-80) cc_final: 0.8066 (m-80) REVERT: A 551 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.8037 (m-40) REVERT: A 582 GLU cc_start: 0.7885 (tt0) cc_final: 0.7036 (tm-30) REVERT: A 657 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7657 (tm-30) REVERT: D 128 ASN cc_start: 0.8456 (m-40) cc_final: 0.8175 (m-40) REVERT: D 190 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.6745 (mp10) REVERT: D 196 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7206 (ttmt) REVERT: D 351 ARG cc_start: 0.7974 (ttm-80) cc_final: 0.7417 (tpp-160) REVERT: D 360 ILE cc_start: 0.6877 (mm) cc_final: 0.6498 (tp) REVERT: D 381 GLU cc_start: 0.7411 (mm-30) cc_final: 0.6943 (pp20) REVERT: D 387 MET cc_start: 0.6346 (tmm) cc_final: 0.5696 (tmm) REVERT: D 398 MET cc_start: 0.5699 (mmm) cc_final: 0.4787 (mmm) REVERT: D 426 LYS cc_start: 0.8382 (mmmt) cc_final: 0.8088 (mmmt) REVERT: B 449 TYR cc_start: 0.8845 (m-10) cc_final: 0.8461 (m-10) REVERT: B 471 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7026 (tm-30) REVERT: B 472 LYS cc_start: 0.8376 (ptpt) cc_final: 0.6833 (ptpt) REVERT: B 612 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8285 (mm-30) outliers start: 52 outliers final: 35 residues processed: 197 average time/residue: 0.1107 time to fit residues: 31.9891 Evaluate side-chains 196 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 152 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 623 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 120 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 86 optimal weight: 0.6980 chunk 62 optimal weight: 0.3980 chunk 60 optimal weight: 0.6980 chunk 135 optimal weight: 0.0170 chunk 122 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.183464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.138510 restraints weight = 15840.839| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.28 r_work: 0.3578 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13052 Z= 0.115 Angle : 0.528 8.634 17790 Z= 0.290 Chirality : 0.039 0.151 1928 Planarity : 0.003 0.049 2110 Dihedral : 16.402 146.131 2124 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.57 % Allowed : 26.47 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.53 (0.23), residues: 1444 helix: 0.88 (0.23), residues: 548 sheet: -2.19 (0.41), residues: 166 loop : -0.80 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 275 TYR 0.012 0.001 TYR D 334 PHE 0.018 0.001 PHE D 350 TRP 0.009 0.001 TRP B 673 HIS 0.009 0.001 HIS A 621 Details of bonding type rmsd covalent geometry : bond 0.00265 (13052) covalent geometry : angle 0.52798 (17790) hydrogen bonds : bond 0.02904 ( 502) hydrogen bonds : angle 4.30332 ( 1362) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 148 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 99 ASP cc_start: 0.8535 (m-30) cc_final: 0.8156 (t70) REVERT: C 258 THR cc_start: 0.8225 (m) cc_final: 0.7653 (p) REVERT: C 286 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7681 (tm-30) REVERT: C 324 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.7994 (mp) REVERT: A 431 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7401 (pp) REVERT: A 452 MET cc_start: 0.7890 (mtt) cc_final: 0.7669 (mtt) REVERT: A 475 GLU cc_start: 0.6345 (mm-30) cc_final: 0.6079 (mm-30) REVERT: A 551 ASN cc_start: 0.8332 (OUTLIER) cc_final: 0.7846 (m-40) REVERT: A 582 GLU cc_start: 0.7847 (tt0) cc_final: 0.6962 (tm-30) REVERT: A 657 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: D 128 ASN cc_start: 0.8463 (m-40) cc_final: 0.8190 (m110) REVERT: D 190 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.6741 (mp10) REVERT: D 196 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7153 (ttmt) REVERT: D 351 ARG cc_start: 0.7886 (ttm-80) cc_final: 0.7377 (tpp-160) REVERT: D 381 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6830 (pp20) REVERT: D 387 MET cc_start: 0.6248 (tmm) cc_final: 0.5665 (tmm) REVERT: D 398 MET cc_start: 0.5778 (mmm) cc_final: 0.4757 (mmm) REVERT: D 426 LYS cc_start: 0.8293 (mmmt) cc_final: 0.8012 (mmmt) REVERT: B 449 TYR cc_start: 0.8833 (m-10) cc_final: 0.8442 (m-10) REVERT: B 471 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6919 (tm-30) REVERT: B 612 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8211 (mm-30) outliers start: 45 outliers final: 32 residues processed: 185 average time/residue: 0.1044 time to fit residues: 28.5314 Evaluate side-chains 188 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 148 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 539 ARG Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 623 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 114 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 50 optimal weight: 0.0040 chunk 61 optimal weight: 0.6980 chunk 120 optimal weight: 0.4980 chunk 145 optimal weight: 3.9990 overall best weight: 1.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 283 ASN ** A 495 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 = 0.4147 r_free = 0.4147 target = 0.181572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.136189 restraints weight = 16023.472| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.51 r_work: 0.3530 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13052 Z= 0.170 Angle : 0.557 8.107 17790 Z= 0.304 Chirality : 0.040 0.217 1928 Planarity : 0.003 0.051 2110 Dihedral : 16.452 147.180 2124 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.17 % Allowed : 27.18 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.59 (0.23), residues: 1444 helix: 0.80 (0.23), residues: 548 sheet: -2.21 (0.41), residues: 166 loop : -0.81 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 287 TYR 0.015 0.001 TYR C 334 PHE 0.016 0.001 PHE A 581 TRP 0.012 0.001 TRP B 673 HIS 0.009 0.001 HIS A 621 Details of bonding type rmsd covalent geometry : bond 0.00401 (13052) covalent geometry : angle 0.55668 (17790) hydrogen bonds : bond 0.03249 ( 502) hydrogen bonds : angle 4.38056 ( 1362) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 99 ASP cc_start: 0.8539 (m-30) cc_final: 0.8194 (t70) REVERT: C 258 THR cc_start: 0.8328 (m) cc_final: 0.7751 (p) REVERT: C 286 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7638 (tm-30) REVERT: C 324 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8084 (mp) REVERT: A 431 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7250 (pp) REVERT: A 432 HIS cc_start: 0.8487 (OUTLIER) cc_final: 0.7985 (m90) REVERT: A 549 TYR cc_start: 0.8521 (m-80) cc_final: 0.7943 (m-80) REVERT: A 551 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.7977 (m-40) REVERT: A 582 GLU cc_start: 0.7919 (tt0) cc_final: 0.7021 (tm-30) REVERT: A 657 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7644 (tm-30) REVERT: D 128 ASN cc_start: 0.8482 (m-40) cc_final: 0.8196 (m110) REVERT: D 190 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.6576 (mp10) REVERT: D 196 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7129 (ttmt) REVERT: D 351 ARG cc_start: 0.7929 (ttm-80) cc_final: 0.7430 (tpp-160) REVERT: D 360 ILE cc_start: 0.6836 (mm) cc_final: 0.6443 (tp) REVERT: D 381 GLU cc_start: 0.7393 (mm-30) cc_final: 0.6852 (pp20) REVERT: D 387 MET cc_start: 0.6311 (tmm) cc_final: 0.5693 (tmm) REVERT: D 398 MET cc_start: 0.5701 (mmm) cc_final: 0.4791 (mmm) REVERT: B 449 TYR cc_start: 0.8860 (m-10) cc_final: 0.8448 (m-10) REVERT: B 471 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.6994 (tm-30) REVERT: B 612 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8264 (mm-30) REVERT: B 624 ARG cc_start: 0.7846 (ttp80) cc_final: 0.7548 (ttp80) outliers start: 40 outliers final: 29 residues processed: 184 average time/residue: 0.1098 time to fit residues: 29.2626 Evaluate side-chains 184 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 623 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 68 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 142 optimal weight: 0.0970 chunk 2 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.184100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.139221 restraints weight = 15845.754| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.24 r_work: 0.3567 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13052 Z= 0.120 Angle : 0.532 8.413 17790 Z= 0.291 Chirality : 0.039 0.216 1928 Planarity : 0.003 0.049 2110 Dihedral : 16.436 145.892 2124 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.17 % Allowed : 27.02 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.49 (0.23), residues: 1444 helix: 0.89 (0.23), residues: 548 sheet: -2.20 (0.41), residues: 166 loop : -0.75 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 351 TYR 0.011 0.001 TYR C 334 PHE 0.019 0.001 PHE D 350 TRP 0.010 0.001 TRP B 673 HIS 0.009 0.001 HIS A 621 Details of bonding type rmsd covalent geometry : bond 0.00276 (13052) covalent geometry : angle 0.53219 (17790) hydrogen bonds : bond 0.02890 ( 502) hydrogen bonds : angle 4.28546 ( 1362) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3936.22 seconds wall clock time: 67 minutes 49.89 seconds (4069.89 seconds total)