Starting phenix.real_space_refine on Sat Oct 11 02:25:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x1q_37998/10_2025/8x1q_37998_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x1q_37998/10_2025/8x1q_37998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x1q_37998/10_2025/8x1q_37998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x1q_37998/10_2025/8x1q_37998.map" model { file = "/net/cci-nas-00/data/ceres_data/8x1q_37998/10_2025/8x1q_37998_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x1q_37998/10_2025/8x1q_37998_neut_trim.cif" } resolution = 2.29 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= 0.001 sd= 0.108 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 7137 2.51 5 N 1778 2.21 5 O 1921 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 126 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10875 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5426 Classifications: {'peptide': 702} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 670} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'HIS:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 5437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5437 Classifications: {'peptide': 702} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 670} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'BCT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'BCT': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.97, per 1000 atoms: 0.27 Number of scatterers: 10875 At special positions: 0 Unit cell: (106.248, 91.336, 130.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1921 8.00 N 1778 7.00 C 7137 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: 0.87 Conformation dependent library (CDL) restraints added in 519.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2628 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 4 sheets defined 67.5% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 17 through 25 Processing helix chain 'A' and resid 34 through 44 removed outlier: 3.945A pdb=" N VAL A 41 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N CYS A 42 " --> pdb=" O HIS A 38 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N CYS A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 58 removed outlier: 3.591A pdb=" N ARG A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 64 Processing helix chain 'A' and resid 68 through 98 removed outlier: 5.632A pdb=" N LEU A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N SER A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 120 Proline residue: A 112 - end of helix removed outlier: 4.026A pdb=" N PHE A 118 " --> pdb=" O ILE A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 147 Processing helix chain 'A' and resid 169 through 196 Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.560A pdb=" N LEU A 205 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 225 Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.525A pdb=" N ILE A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 252 Processing helix chain 'A' and resid 253 through 257 removed outlier: 3.729A pdb=" N THR A 257 " --> pdb=" O ILE A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 282 removed outlier: 3.678A pdb=" N LEU A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 307 Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 332 through 339 Processing helix chain 'A' and resid 339 through 366 removed outlier: 3.559A pdb=" N VAL A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 388 Processing helix chain 'A' and resid 396 through 406 Processing helix chain 'A' and resid 411 through 427 Processing helix chain 'A' and resid 428 through 433 removed outlier: 3.549A pdb=" N LEU A 432 " --> pdb=" O GLY A 429 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A 433 " --> pdb=" O PHE A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 447 removed outlier: 3.882A pdb=" N LEU A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 456 through 465 removed outlier: 3.851A pdb=" N ARG A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 463 " --> pdb=" O GLY A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 485 through 503 removed outlier: 3.840A pdb=" N ALA A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE A 499 " --> pdb=" O GLN A 495 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A 503 " --> pdb=" O ILE A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 Processing helix chain 'A' and resid 563 through 584 Processing helix chain 'A' and resid 612 through 618 removed outlier: 3.706A pdb=" N VAL A 615 " --> pdb=" O GLN A 612 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 616 " --> pdb=" O ILE A 613 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN A 618 " --> pdb=" O VAL A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 676 Processing helix chain 'A' and resid 687 through 697 removed outlier: 3.665A pdb=" N ILE A 691 " --> pdb=" O ASP A 687 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN A 695 " --> pdb=" O ILE A 691 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG A 696 " --> pdb=" O GLU A 692 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR A 697 " --> pdb=" O LYS A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 707 No H-bonds generated for 'chain 'A' and resid 705 through 707' Processing helix chain 'A' and resid 712 through 725 Processing helix chain 'B' and resid 17 through 23 Processing helix chain 'B' and resid 34 through 43 removed outlier: 4.092A pdb=" N CYS B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 58 removed outlier: 3.926A pdb=" N ARG B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 64 removed outlier: 3.575A pdb=" N TRP B 63 " --> pdb=" O PRO B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 99 removed outlier: 5.462A pdb=" N LEU B 74 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N SER B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 82 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 96 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 109 removed outlier: 3.619A pdb=" N TYR B 107 " --> pdb=" O VAL B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 120 removed outlier: 3.518A pdb=" N ILE B 114 " --> pdb=" O PHE B 110 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE B 118 " --> pdb=" O ILE B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 146 Processing helix chain 'B' and resid 169 through 196 Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.560A pdb=" N VAL B 201 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL B 202 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR B 204 " --> pdb=" O VAL B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 231 removed outlier: 3.790A pdb=" N LEU B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LYS B 227 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N PHE B 228 " --> pdb=" O SER B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 252 removed outlier: 3.522A pdb=" N LYS B 245 " --> pdb=" O VAL B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 257 removed outlier: 3.638A pdb=" N THR B 257 " --> pdb=" O ILE B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 282 removed outlier: 3.696A pdb=" N ILE B 274 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN B 280 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 307 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 332 through 339 Processing helix chain 'B' and resid 339 through 365 removed outlier: 3.702A pdb=" N GLY B 345 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR B 361 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 396 through 406 removed outlier: 3.502A pdb=" N VAL B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 427 removed outlier: 3.556A pdb=" N ALA B 418 " --> pdb=" O GLY B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 removed outlier: 3.501A pdb=" N LEU B 431 " --> pdb=" O ILE B 428 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 433 " --> pdb=" O PHE B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 446 removed outlier: 3.883A pdb=" N LEU B 440 " --> pdb=" O GLN B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 456 through 465 Processing helix chain 'B' and resid 465 through 483 Processing helix chain 'B' and resid 483 through 504 removed outlier: 3.931A pdb=" N LEU B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA B 489 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE B 499 " --> pdb=" O GLN B 495 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 503 " --> pdb=" O ILE B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 561 Processing helix chain 'B' and resid 563 through 584 Processing helix chain 'B' and resid 612 through 618 removed outlier: 3.600A pdb=" N VAL B 615 " --> pdb=" O GLN B 612 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN B 618 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 677 removed outlier: 3.535A pdb=" N SER B 669 " --> pdb=" O ARG B 665 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE B 670 " --> pdb=" O GLY B 666 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE B 677 " --> pdb=" O GLU B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 697 removed outlier: 3.549A pdb=" N ILE B 691 " --> pdb=" O ASP B 687 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN B 695 " --> pdb=" O ILE B 691 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG B 696 " --> pdb=" O GLU B 692 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR B 697 " --> pdb=" O LYS B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 707 No H-bonds generated for 'chain 'B' and resid 705 through 707' Processing helix chain 'B' and resid 712 through 724 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 14 Processing sheet with id=AA2, first strand: chain 'A' and resid 520 through 522 removed outlier: 4.952A pdb=" N ILE A 537 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 9.452A pdb=" N ASN A 513 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 13.274A pdb=" N VAL A 535 " --> pdb=" O ASN A 513 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LYS A 536 " --> pdb=" O ILE A 650 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ASP A 652 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE A 538 " --> pdb=" O ASP A 652 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N PHE A 710 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE A 683 " --> pdb=" O PHE A 710 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 127 through 128 Processing sheet with id=AA4, first strand: chain 'B' and resid 520 through 522 removed outlier: 4.954A pdb=" N ILE B 537 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 9.256A pdb=" N ASN B 513 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 13.238A pdb=" N VAL B 535 " --> pdb=" O ASN B 513 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LYS B 536 " --> pdb=" O ILE B 650 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ASP B 652 " --> pdb=" O LYS B 536 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N PHE B 538 " --> pdb=" O ASP B 652 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N PHE B 710 " --> pdb=" O VAL B 681 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE B 683 " --> pdb=" O PHE B 710 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1848 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.78 Time building geometry restraints manager: 1.18 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: 2058 1.32 - 1.45: 2565 1.45 - 1.57: 6422 1.57 - 1.69: 0 1.69 - 1.81: 59 Bond restraints: 11104 Sorted by residual: bond pdb=" C CYS A 540 " pdb=" O CYS A 540 " ideal model delta sigma weight residual 1.246 1.216 0.030 9.20e-03 1.18e+04 1.09e+01 bond pdb=" C BCT A 801 " pdb=" O3 BCT A 801 " ideal model delta sigma weight residual 1.389 1.324 0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C BCT B 801 " pdb=" O3 BCT B 801 " ideal model delta sigma weight residual 1.389 1.327 0.062 2.00e-02 2.50e+03 9.59e+00 bond pdb=" CA LEU B 415 " pdb=" C LEU B 415 " ideal model delta sigma weight residual 1.524 1.563 -0.040 1.29e-02 6.01e+03 9.55e+00 bond pdb=" C LEU B 671 " pdb=" O LEU B 671 " ideal model delta sigma weight residual 1.236 1.201 0.035 1.15e-02 7.56e+03 9.27e+00 ... (remaining 11099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 14001 2.25 - 4.50: 899 4.50 - 6.76: 132 6.76 - 9.01: 41 9.01 - 11.26: 9 Bond angle restraints: 15082 Sorted by residual: angle pdb=" N VAL B 481 " pdb=" CA VAL B 481 " pdb=" C VAL B 481 " ideal model delta sigma weight residual 110.72 119.65 -8.93 1.01e+00 9.80e-01 7.82e+01 angle pdb=" N PHE B 118 " pdb=" CA PHE B 118 " pdb=" C PHE B 118 " ideal model delta sigma weight residual 111.36 120.54 -9.18 1.09e+00 8.42e-01 7.09e+01 angle pdb=" N ALA B 427 " pdb=" CA ALA B 427 " pdb=" C ALA B 427 " ideal model delta sigma weight residual 114.04 124.19 -10.15 1.24e+00 6.50e-01 6.70e+01 angle pdb=" N ILE B 428 " pdb=" CA ILE B 428 " pdb=" C ILE B 428 " ideal model delta sigma weight residual 111.88 120.30 -8.42 1.06e+00 8.90e-01 6.31e+01 angle pdb=" N ASP A 366 " pdb=" CA ASP A 366 " pdb=" C ASP A 366 " ideal model delta sigma weight residual 111.02 120.58 -9.56 1.25e+00 6.40e-01 5.85e+01 ... (remaining 15077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.55: 5956 16.55 - 33.11: 517 33.11 - 49.66: 105 49.66 - 66.22: 22 66.22 - 82.77: 4 Dihedral angle restraints: 6604 sinusoidal: 2536 harmonic: 4068 Sorted by residual: dihedral pdb=" C VAL A 241 " pdb=" N VAL A 241 " pdb=" CA VAL A 241 " pdb=" CB VAL A 241 " ideal model delta harmonic sigma weight residual -122.00 -135.09 13.09 0 2.50e+00 1.60e-01 2.74e+01 dihedral pdb=" C ASP A 701 " pdb=" N ASP A 701 " pdb=" CA ASP A 701 " pdb=" CB ASP A 701 " ideal model delta harmonic sigma weight residual -122.60 -109.73 -12.87 0 2.50e+00 1.60e-01 2.65e+01 dihedral pdb=" C ASP B 701 " pdb=" N ASP B 701 " pdb=" CA ASP B 701 " pdb=" CB ASP B 701 " ideal model delta harmonic sigma weight residual -122.60 -109.90 -12.70 0 2.50e+00 1.60e-01 2.58e+01 ... (remaining 6601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1443 0.102 - 0.203: 260 0.203 - 0.305: 70 0.305 - 0.406: 20 0.406 - 0.508: 7 Chirality restraints: 1800 Sorted by residual: chirality pdb=" CA GLU B 606 " pdb=" N GLU B 606 " pdb=" C GLU B 606 " pdb=" CB GLU B 606 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.45e+00 chirality pdb=" CA LYS B 678 " pdb=" N LYS B 678 " pdb=" C LYS B 678 " pdb=" CB LYS B 678 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" CA THR B 214 " pdb=" N THR B 214 " pdb=" C THR B 214 " pdb=" CB THR B 214 " both_signs ideal model delta sigma weight residual False 2.53 2.08 0.45 2.00e-01 2.50e+01 5.01e+00 ... (remaining 1797 not shown) Planarity restraints: 1885 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 701 " -0.020 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C ASP A 701 " 0.069 2.00e-02 2.50e+03 pdb=" O ASP A 701 " -0.026 2.00e-02 2.50e+03 pdb=" N GLY A 702 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 116 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.81e+00 pdb=" C TYR B 116 " -0.054 2.00e-02 2.50e+03 pdb=" O TYR B 116 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU B 117 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 13 " -0.037 5.00e-02 4.00e+02 5.60e-02 5.01e+00 pdb=" N PRO A 14 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 14 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 14 " -0.031 5.00e-02 4.00e+02 ... (remaining 1882 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1085 2.74 - 3.28: 10427 3.28 - 3.82: 16287 3.82 - 4.36: 20193 4.36 - 4.90: 34171 Nonbonded interactions: 82163 Sorted by model distance: nonbonded pdb=" NH1 ARG B 576 " pdb=" OE1 GLU B 606 " model vdw 2.206 3.120 nonbonded pdb=" O ASN B 322 " pdb=" OD1 ASN B 322 " model vdw 2.211 3.040 nonbonded pdb=" O THR A 18 " pdb=" OE1 GLU A 22 " model vdw 2.216 3.040 nonbonded pdb=" OG SER A 75 " pdb=" O GLY A 407 " model vdw 2.257 3.040 nonbonded pdb=" O ILE B 544 " pdb=" OG SER B 663 " model vdw 2.362 3.040 ... (remaining 82158 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 7 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 801)) selection = (chain 'B' and (resid 7 through 30 or (resid 31 through 33 and (name N or name C \ A or name C or name O or name CB )) or resid 34 through 589 or (resid 590 and (n \ ame N or name CA or name C or name O or name CB )) or resid 591 through 595 or ( \ resid 596 through 603 and (name N or name CA or name C or name O or name CB )) o \ r resid 604 or (resid 605 and (name N or name CA or name C or name O or name CB \ )) or resid 606 through 636 or (resid 637 and (name N or name CA or name C or na \ me O or name CB )) or resid 638 through 801)) } 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: 2.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.610 Find NCS groups from input model: 0.200 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:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 11104 Z= 0.522 Angle : 1.264 11.259 15082 Z= 0.891 Chirality : 0.095 0.508 1800 Planarity : 0.006 0.056 1885 Dihedral : 12.909 82.771 3976 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.53 % Allowed : 9.41 % Favored : 89.07 % Cbeta Deviations : 0.76 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: -0.41 (0.21), residues: 1396 helix: 0.48 (0.17), residues: 866 sheet: 2.95 (0.75), residues: 36 loop : -1.85 (0.24), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 576 TYR 0.023 0.002 TYR A 9 PHE 0.024 0.002 PHE A 313 TRP 0.015 0.002 TRP A 63 HIS 0.007 0.002 HIS A 647 Details of bonding type rmsd covalent geometry : bond 0.00769 (11104) covalent geometry : angle 1.26371 (15082) hydrogen bonds : bond 0.29297 ( 630) hydrogen bonds : angle 6.11325 ( 1848) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 283 LYS cc_start: 0.7567 (tttt) cc_final: 0.7326 (ttpp) REVERT: A 322 ASN cc_start: 0.7754 (p0) cc_final: 0.7398 (p0) REVERT: A 451 MET cc_start: 0.8460 (mtm) cc_final: 0.8073 (mtm) REVERT: A 618 GLN cc_start: 0.8294 (mm-40) cc_final: 0.8051 (mm-40) REVERT: B 24 ASN cc_start: 0.8441 (m-40) cc_final: 0.8208 (m110) REVERT: B 70 LYS cc_start: 0.8312 (tttt) cc_final: 0.7813 (tmtt) REVERT: B 332 ASP cc_start: 0.7868 (t0) cc_final: 0.7533 (m-30) REVERT: B 629 ILE cc_start: 0.7884 (mt) cc_final: 0.7658 (mt) REVERT: B 678 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8760 (mmtm) outliers start: 18 outliers final: 8 residues processed: 145 average time/residue: 0.6784 time to fit residues: 104.9540 Evaluate side-chains 100 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 678 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 231 GLN A 279 ASN A 337 GLN A 411 GLN A 454 GLN A 582 GLN A 612 GLN A 632 ASN A 672 GLN A 714 HIS B 7 ASN B 19 ASN B 48 GLN B 231 GLN B 279 ASN B 280 GLN B 326 GLN B 337 GLN B 403 GLN B 454 GLN B 495 GLN B 513 ASN B 584 GLN B 612 GLN B 672 GLN B 714 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.141823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.105062 restraints weight = 12246.587| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.91 r_work: 0.3213 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11104 Z= 0.161 Angle : 0.602 9.323 15082 Z= 0.332 Chirality : 0.044 0.170 1800 Planarity : 0.005 0.054 1885 Dihedral : 5.390 50.851 1509 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.20 % Allowed : 10.34 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 1.12 (0.22), residues: 1396 helix: 1.84 (0.18), residues: 856 sheet: 3.33 (0.81), residues: 36 loop : -1.47 (0.23), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 389 TYR 0.022 0.002 TYR B 9 PHE 0.017 0.001 PHE B 130 TRP 0.015 0.002 TRP A 63 HIS 0.003 0.001 HIS B 647 Details of bonding type rmsd covalent geometry : bond 0.00291 (11104) covalent geometry : angle 0.60205 (15082) hydrogen bonds : bond 0.07940 ( 630) hydrogen bonds : angle 4.22176 ( 1848) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 322 ASN cc_start: 0.7814 (p0) cc_final: 0.7454 (p0) REVERT: A 329 ILE cc_start: 0.8168 (pt) cc_final: 0.7925 (pp) REVERT: A 580 LYS cc_start: 0.7365 (tttm) cc_final: 0.7078 (ttpp) REVERT: A 689 ASP cc_start: 0.7562 (m-30) cc_final: 0.7267 (m-30) REVERT: B 42 CYS cc_start: 0.4438 (OUTLIER) cc_final: 0.4232 (m) REVERT: B 170 ASP cc_start: 0.6136 (OUTLIER) cc_final: 0.5649 (t0) REVERT: B 270 LEU cc_start: 0.7805 (tt) cc_final: 0.7587 (tp) REVERT: B 332 ASP cc_start: 0.8123 (t0) cc_final: 0.7583 (t70) REVERT: B 678 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8654 (mmtt) outliers start: 26 outliers final: 6 residues processed: 123 average time/residue: 0.5979 time to fit residues: 79.1593 Evaluate side-chains 98 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 678 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 7 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 63 optimal weight: 0.0370 chunk 93 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 52 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 55 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 overall best weight: 1.2060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN A 611 ASN A 612 GLN B 24 ASN B 311 ASN B 612 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.139071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.101766 restraints weight = 12363.325| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.91 r_work: 0.3167 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11104 Z= 0.162 Angle : 0.566 8.375 15082 Z= 0.316 Chirality : 0.043 0.147 1800 Planarity : 0.005 0.056 1885 Dihedral : 4.857 49.262 1503 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.12 % Allowed : 11.61 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 1.36 (0.22), residues: 1396 helix: 2.10 (0.18), residues: 852 sheet: 3.49 (0.76), residues: 36 loop : -1.47 (0.23), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 173 TYR 0.024 0.002 TYR B 9 PHE 0.018 0.002 PHE A 130 TRP 0.013 0.001 TRP A 63 HIS 0.005 0.001 HIS B 647 Details of bonding type rmsd covalent geometry : bond 0.00299 (11104) covalent geometry : angle 0.56649 (15082) hydrogen bonds : bond 0.08297 ( 630) hydrogen bonds : angle 4.11402 ( 1848) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 322 ASN cc_start: 0.7704 (p0) cc_final: 0.7376 (p0) REVERT: A 329 ILE cc_start: 0.8322 (pt) cc_final: 0.8008 (pp) REVERT: A 514 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8511 (tp) REVERT: A 580 LYS cc_start: 0.7374 (tttm) cc_final: 0.7015 (ttpp) REVERT: A 689 ASP cc_start: 0.7700 (m-30) cc_final: 0.7417 (m-30) REVERT: B 24 ASN cc_start: 0.8627 (m-40) cc_final: 0.8356 (m110) REVERT: B 332 ASP cc_start: 0.8078 (t0) cc_final: 0.7357 (m-30) REVERT: B 579 ARG cc_start: 0.7465 (mtt180) cc_final: 0.7201 (mtt-85) REVERT: B 614 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7081 (mp0) outliers start: 25 outliers final: 11 residues processed: 113 average time/residue: 0.6333 time to fit residues: 77.0512 Evaluate side-chains 99 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 614 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 68 optimal weight: 0.0980 chunk 99 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 612 GLN B 311 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.132442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.094882 restraints weight = 12228.370| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.90 r_work: 0.3065 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 11104 Z= 0.283 Angle : 0.761 9.484 15082 Z= 0.426 Chirality : 0.051 0.179 1800 Planarity : 0.007 0.065 1885 Dihedral : 5.240 56.007 1499 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.71 % Allowed : 11.61 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 0.76 (0.22), residues: 1396 helix: 1.56 (0.18), residues: 850 sheet: 3.23 (0.73), residues: 38 loop : -1.60 (0.23), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 399 TYR 0.030 0.003 TYR A 9 PHE 0.021 0.003 PHE B 391 TRP 0.012 0.002 TRP A 63 HIS 0.008 0.002 HIS A 647 Details of bonding type rmsd covalent geometry : bond 0.00637 (11104) covalent geometry : angle 0.76150 (15082) hydrogen bonds : bond 0.12334 ( 630) hydrogen bonds : angle 4.48644 ( 1848) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 0.460 Fit side-chains REVERT: A 322 ASN cc_start: 0.7701 (p0) cc_final: 0.7355 (p0) REVERT: A 514 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8548 (tp) REVERT: A 689 ASP cc_start: 0.7832 (m-30) cc_final: 0.7494 (m-30) REVERT: B 24 ASN cc_start: 0.8686 (m-40) cc_final: 0.8405 (m110) REVERT: B 207 GLU cc_start: 0.8284 (pt0) cc_final: 0.7567 (tm-30) REVERT: B 270 LEU cc_start: 0.7809 (tt) cc_final: 0.7581 (tp) REVERT: B 332 ASP cc_start: 0.8233 (t0) cc_final: 0.7663 (t70) REVERT: B 516 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7437 (mpt180) REVERT: B 579 ARG cc_start: 0.7511 (mtt180) cc_final: 0.7226 (mtt-85) outliers start: 32 outliers final: 16 residues processed: 118 average time/residue: 0.6681 time to fit residues: 84.6708 Evaluate side-chains 107 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 516 ARG Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 533 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 63 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 104 optimal weight: 0.4980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN A 612 GLN B 311 ASN B 612 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.140753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.103775 restraints weight = 12399.207| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.92 r_work: 0.3197 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11104 Z= 0.138 Angle : 0.523 8.141 15082 Z= 0.291 Chirality : 0.042 0.152 1800 Planarity : 0.005 0.060 1885 Dihedral : 4.793 47.933 1499 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.12 % Allowed : 12.46 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 1.43 (0.22), residues: 1396 helix: 2.15 (0.18), residues: 862 sheet: 3.45 (0.75), residues: 36 loop : -1.53 (0.23), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 173 TYR 0.019 0.001 TYR A 9 PHE 0.017 0.001 PHE B 282 TRP 0.014 0.001 TRP A 63 HIS 0.005 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00243 (11104) covalent geometry : angle 0.52267 (15082) hydrogen bonds : bond 0.06935 ( 630) hydrogen bonds : angle 4.07310 ( 1848) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.447 Fit side-chains REVERT: A 322 ASN cc_start: 0.7646 (p0) cc_final: 0.7317 (p0) REVERT: A 514 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8470 (tp) REVERT: A 689 ASP cc_start: 0.7702 (m-30) cc_final: 0.7427 (m-30) REVERT: B 24 ASN cc_start: 0.8661 (m-40) cc_final: 0.8371 (m110) REVERT: B 270 LEU cc_start: 0.7769 (tt) cc_final: 0.7533 (tp) REVERT: B 332 ASP cc_start: 0.8029 (t0) cc_final: 0.7349 (m-30) REVERT: B 516 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7330 (mpt180) REVERT: B 579 ARG cc_start: 0.7090 (mtt180) cc_final: 0.6867 (mtt-85) outliers start: 25 outliers final: 15 residues processed: 107 average time/residue: 0.5858 time to fit residues: 67.9573 Evaluate side-chains 101 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 516 ARG Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 615 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 84 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 57 optimal weight: 20.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN B 311 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.139638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.102412 restraints weight = 12327.812| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.92 r_work: 0.3177 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11104 Z= 0.144 Angle : 0.522 7.275 15082 Z= 0.291 Chirality : 0.042 0.150 1800 Planarity : 0.005 0.059 1885 Dihedral : 4.623 44.947 1499 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.78 % Allowed : 13.14 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 1.59 (0.22), residues: 1396 helix: 2.27 (0.18), residues: 860 sheet: 3.77 (0.76), residues: 34 loop : -1.42 (0.24), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 13 TYR 0.022 0.001 TYR A 9 PHE 0.018 0.001 PHE A 130 TRP 0.011 0.001 TRP A 63 HIS 0.004 0.001 HIS A 647 Details of bonding type rmsd covalent geometry : bond 0.00264 (11104) covalent geometry : angle 0.52200 (15082) hydrogen bonds : bond 0.07359 ( 630) hydrogen bonds : angle 4.00547 ( 1848) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.499 Fit side-chains REVERT: A 322 ASN cc_start: 0.7727 (p0) cc_final: 0.7396 (p0) REVERT: A 514 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8449 (tp) REVERT: A 689 ASP cc_start: 0.7800 (m-30) cc_final: 0.7475 (m-30) REVERT: B 24 ASN cc_start: 0.8679 (m-40) cc_final: 0.8364 (m110) REVERT: B 270 LEU cc_start: 0.7773 (tt) cc_final: 0.7544 (tp) REVERT: B 332 ASP cc_start: 0.8011 (t0) cc_final: 0.7339 (m-30) REVERT: B 516 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7341 (mpt180) REVERT: B 580 LYS cc_start: 0.7264 (tttp) cc_final: 0.6510 (tttp) outliers start: 21 outliers final: 15 residues processed: 103 average time/residue: 0.6413 time to fit residues: 71.2005 Evaluate side-chains 100 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 516 ARG Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 615 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 105 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 88 optimal weight: 0.4980 chunk 8 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 130 optimal weight: 0.0040 chunk 55 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN B 311 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.139420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.102213 restraints weight = 12285.248| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.91 r_work: 0.3173 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11104 Z= 0.146 Angle : 0.527 7.057 15082 Z= 0.293 Chirality : 0.042 0.150 1800 Planarity : 0.005 0.059 1885 Dihedral : 4.561 42.568 1499 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.95 % Allowed : 12.71 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 1.65 (0.22), residues: 1396 helix: 2.29 (0.18), residues: 860 sheet: 3.65 (0.73), residues: 36 loop : -1.35 (0.24), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 399 TYR 0.022 0.002 TYR A 9 PHE 0.018 0.001 PHE A 130 TRP 0.012 0.001 TRP A 63 HIS 0.004 0.001 HIS B 647 Details of bonding type rmsd covalent geometry : bond 0.00270 (11104) covalent geometry : angle 0.52654 (15082) hydrogen bonds : bond 0.07420 ( 630) hydrogen bonds : angle 3.99860 ( 1848) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.431 Fit side-chains REVERT: A 322 ASN cc_start: 0.7720 (p0) cc_final: 0.7393 (p0) REVERT: A 514 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8414 (tp) REVERT: A 689 ASP cc_start: 0.7787 (m-30) cc_final: 0.7455 (m-30) REVERT: B 24 ASN cc_start: 0.8649 (m-40) cc_final: 0.8324 (m110) REVERT: B 270 LEU cc_start: 0.7785 (tt) cc_final: 0.7541 (tp) REVERT: B 332 ASP cc_start: 0.8010 (t0) cc_final: 0.7335 (m-30) REVERT: B 516 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7341 (mpt180) REVERT: B 580 LYS cc_start: 0.7330 (tttp) cc_final: 0.6566 (tttp) REVERT: B 611 ASN cc_start: 0.8208 (OUTLIER) cc_final: 0.7835 (t0) outliers start: 23 outliers final: 15 residues processed: 98 average time/residue: 0.6762 time to fit residues: 71.2162 Evaluate side-chains 94 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 516 ARG Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 615 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN B 311 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.135557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.099030 restraints weight = 12237.453| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.05 r_work: 0.3109 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11104 Z= 0.198 Angle : 0.614 7.485 15082 Z= 0.343 Chirality : 0.045 0.159 1800 Planarity : 0.005 0.062 1885 Dihedral : 4.761 44.849 1498 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.61 % Allowed : 12.71 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 1.31 (0.22), residues: 1396 helix: 2.03 (0.18), residues: 848 sheet: 3.24 (0.73), residues: 38 loop : -1.42 (0.23), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 539 TYR 0.027 0.002 TYR A 9 PHE 0.020 0.002 PHE A 130 TRP 0.010 0.002 TRP A 63 HIS 0.007 0.001 HIS B 647 Details of bonding type rmsd covalent geometry : bond 0.00412 (11104) covalent geometry : angle 0.61431 (15082) hydrogen bonds : bond 0.09599 ( 630) hydrogen bonds : angle 4.19640 ( 1848) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.471 Fit side-chains REVERT: A 322 ASN cc_start: 0.7726 (p0) cc_final: 0.7392 (p0) REVERT: A 514 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8477 (tp) REVERT: A 689 ASP cc_start: 0.7758 (m-30) cc_final: 0.7433 (m-30) REVERT: B 270 LEU cc_start: 0.7772 (tt) cc_final: 0.7522 (tp) REVERT: B 332 ASP cc_start: 0.8077 (t0) cc_final: 0.7352 (m-30) REVERT: B 516 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7418 (mpt180) REVERT: B 580 LYS cc_start: 0.7467 (tttp) cc_final: 0.6712 (tttp) REVERT: B 611 ASN cc_start: 0.8297 (OUTLIER) cc_final: 0.7945 (t0) outliers start: 19 outliers final: 15 residues processed: 101 average time/residue: 0.6182 time to fit residues: 67.3769 Evaluate side-chains 103 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 516 ARG Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 615 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 72 optimal weight: 0.6980 chunk 127 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN B 24 ASN B 311 ASN B 612 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.138258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.102120 restraints weight = 12186.589| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.01 r_work: 0.3154 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11104 Z= 0.155 Angle : 0.544 7.224 15082 Z= 0.304 Chirality : 0.042 0.155 1800 Planarity : 0.005 0.060 1885 Dihedral : 4.630 43.095 1498 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.69 % Allowed : 12.88 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 1.48 (0.22), residues: 1396 helix: 2.16 (0.18), residues: 852 sheet: 3.54 (0.73), residues: 36 loop : -1.37 (0.24), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 399 TYR 0.023 0.002 TYR A 9 PHE 0.019 0.001 PHE A 130 TRP 0.013 0.001 TRP A 63 HIS 0.005 0.001 HIS B 647 Details of bonding type rmsd covalent geometry : bond 0.00293 (11104) covalent geometry : angle 0.54444 (15082) hydrogen bonds : bond 0.07924 ( 630) hydrogen bonds : angle 4.07302 ( 1848) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.465 Fit side-chains REVERT: A 322 ASN cc_start: 0.7712 (p0) cc_final: 0.7382 (p0) REVERT: A 514 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8437 (tp) REVERT: A 689 ASP cc_start: 0.7720 (m-30) cc_final: 0.7415 (m-30) REVERT: B 24 ASN cc_start: 0.8665 (m-40) cc_final: 0.8383 (m110) REVERT: B 270 LEU cc_start: 0.7745 (tt) cc_final: 0.7489 (tp) REVERT: B 332 ASP cc_start: 0.8020 (t0) cc_final: 0.7314 (m-30) REVERT: B 516 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7396 (mpt180) REVERT: B 580 LYS cc_start: 0.7396 (tttp) cc_final: 0.6643 (tttp) REVERT: B 611 ASN cc_start: 0.8298 (OUTLIER) cc_final: 0.7937 (t0) outliers start: 20 outliers final: 15 residues processed: 93 average time/residue: 0.6112 time to fit residues: 61.3619 Evaluate side-chains 97 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 516 ARG Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 615 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 116 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 57 optimal weight: 20.0000 chunk 9 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 129 optimal weight: 0.0020 chunk 115 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN B 311 ASN B 612 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.143202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.106367 restraints weight = 12258.971| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.92 r_work: 0.3233 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11104 Z= 0.120 Angle : 0.477 6.311 15082 Z= 0.264 Chirality : 0.041 0.146 1800 Planarity : 0.004 0.058 1885 Dihedral : 4.343 38.908 1498 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.36 % Allowed : 13.14 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 1.86 (0.23), residues: 1396 helix: 2.49 (0.18), residues: 860 sheet: 3.81 (0.77), residues: 34 loop : -1.30 (0.24), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 399 TYR 0.017 0.001 TYR A 9 PHE 0.016 0.001 PHE A 130 TRP 0.014 0.001 TRP A 63 HIS 0.003 0.001 HIS B 647 Details of bonding type rmsd covalent geometry : bond 0.00214 (11104) covalent geometry : angle 0.47698 (15082) hydrogen bonds : bond 0.05814 ( 630) hydrogen bonds : angle 3.88726 ( 1848) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.337 Fit side-chains REVERT: A 322 ASN cc_start: 0.7693 (p0) cc_final: 0.7372 (p0) REVERT: A 514 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8450 (tp) REVERT: A 689 ASP cc_start: 0.7823 (m-30) cc_final: 0.7527 (m-30) REVERT: B 270 LEU cc_start: 0.7768 (tt) cc_final: 0.7518 (tp) REVERT: B 332 ASP cc_start: 0.8018 (t0) cc_final: 0.7348 (m-30) REVERT: B 516 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7236 (mpt180) REVERT: B 580 LYS cc_start: 0.7444 (tttp) cc_final: 0.6737 (tttp) REVERT: B 611 ASN cc_start: 0.8241 (OUTLIER) cc_final: 0.7887 (t0) outliers start: 16 outliers final: 10 residues processed: 91 average time/residue: 0.6175 time to fit residues: 60.6741 Evaluate side-chains 85 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 516 ARG Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 615 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 5 optimal weight: 0.0020 chunk 2 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN A 337 GLN B 311 ASN B 612 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.142234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.105240 restraints weight = 12315.773| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.91 r_work: 0.3216 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11104 Z= 0.125 Angle : 0.493 7.635 15082 Z= 0.271 Chirality : 0.041 0.144 1800 Planarity : 0.004 0.057 1885 Dihedral : 4.003 26.203 1495 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.19 % Allowed : 13.64 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 2.01 (0.23), residues: 1396 helix: 2.67 (0.18), residues: 846 sheet: 3.84 (0.76), residues: 34 loop : -1.27 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 389 TYR 0.018 0.001 TYR A 9 PHE 0.017 0.001 PHE A 130 TRP 0.013 0.001 TRP A 63 HIS 0.003 0.001 HIS B 647 Details of bonding type rmsd covalent geometry : bond 0.00227 (11104) covalent geometry : angle 0.49297 (15082) hydrogen bonds : bond 0.06204 ( 630) hydrogen bonds : angle 3.88665 ( 1848) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5037.10 seconds wall clock time: 86 minutes 12.08 seconds (5172.08 seconds total)