Starting phenix.real_space_refine on Tue Jul 29 02:25:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x1q_37998/07_2025/8x1q_37998_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x1q_37998/07_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_37998/07_2025/8x1q_37998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x1q_37998/07_2025/8x1q_37998.map" model { file = "/net/cci-nas-00/data/ceres_data/8x1q_37998/07_2025/8x1q_37998_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x1q_37998/07_2025/8x1q_37998_neut_trim.cif" } resolution = 2.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'ASP:plan': 3, 'HIS:plan': 2} 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: {'GLN:plan1': 1, 'ASP:plan': 3, 'HIS:plan': 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: 7.42, per 1000 atoms: 0.68 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: 2.48 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.06 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: 3.51 Time building geometry restraints manager: 3.00 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 725 or resid 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 725 or resid 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: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.390 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.490 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.21), 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 TRP 0.015 0.002 TRP A 63 HIS 0.007 0.002 HIS A 647 PHE 0.024 0.002 PHE A 313 TYR 0.023 0.002 TYR A 9 ARG 0.005 0.001 ARG A 576 Details of bonding type rmsd hydrogen bonds : bond 0.29297 ( 630) hydrogen bonds : angle 6.11325 ( 1848) covalent geometry : bond 0.00769 (11104) covalent geometry : angle 1.26371 (15082) *********************** 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 : 1.313 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: 0.8207 (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: 1.4561 time to fit residues: 226.0058 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 : 1.172 ------------------------------------------------------------------------------- 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 118 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 58 optimal weight: 0.2980 chunk 36 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 326 GLN 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 611 ASN B 612 GLN B 672 GLN B 714 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.139673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.102705 restraints weight = 12156.648| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.91 r_work: 0.3179 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1992 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= 0.176 Angle : 0.614 9.031 15082 Z= 0.343 Chirality : 0.044 0.151 1800 Planarity : 0.005 0.055 1885 Dihedral : 5.420 53.176 1509 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.03 % Allowed : 10.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.22), residues: 1396 helix: 1.78 (0.18), residues: 856 sheet: 3.30 (0.81), residues: 36 loop : -1.52 (0.23), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 63 HIS 0.004 0.001 HIS B 647 PHE 0.018 0.002 PHE A 130 TYR 0.023 0.002 TYR B 9 ARG 0.003 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.08966 ( 630) hydrogen bonds : angle 4.29164 ( 1848) covalent geometry : bond 0.00316 (11104) covalent geometry : angle 0.61368 (15082) *********************** 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 126 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 2.046 Fit side-chains revert: symmetry clash REVERT: A 322 ASN cc_start: 0.7861 (p0) cc_final: 0.7488 (p0) REVERT: A 329 ILE cc_start: 0.8192 (pt) cc_final: 0.7955 (pp) REVERT: A 451 MET cc_start: 0.8867 (mtm) cc_final: 0.8506 (mtm) REVERT: A 687 ASP cc_start: 0.7522 (p0) cc_final: 0.7319 (p0) REVERT: A 689 ASP cc_start: 0.7608 (m-30) cc_final: 0.7303 (m-30) REVERT: B 42 CYS cc_start: 0.4383 (OUTLIER) cc_final: 0.4112 (m) REVERT: B 170 ASP cc_start: 0.6311 (OUTLIER) cc_final: 0.5814 (t0) REVERT: B 207 GLU cc_start: 0.8056 (pt0) cc_final: 0.7416 (tm-30) REVERT: B 332 ASP cc_start: 0.8145 (t0) cc_final: 0.7610 (t70) REVERT: B 614 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7010 (mp0) REVERT: B 678 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8681 (mmtt) outliers start: 24 outliers final: 9 residues processed: 115 average time/residue: 1.4384 time to fit residues: 178.4705 Evaluate side-chains 105 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 1.266 ------------------------------------------------------------------------------- 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 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 333 VAL Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 614 GLU 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 108 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN A 612 GLN B 24 ASN B 311 ASN B 612 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.135840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.098304 restraints weight = 12251.243| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.91 r_work: 0.3116 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2294 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= 0.199 Angle : 0.640 9.448 15082 Z= 0.358 Chirality : 0.045 0.152 1800 Planarity : 0.006 0.060 1885 Dihedral : 5.100 53.169 1504 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.63 % Allowed : 11.44 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.22), residues: 1396 helix: 1.90 (0.18), residues: 848 sheet: 3.19 (0.72), residues: 38 loop : -1.57 (0.23), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 63 HIS 0.006 0.002 HIS B 647 PHE 0.019 0.002 PHE A 130 TYR 0.027 0.002 TYR B 9 ARG 0.003 0.000 ARG B 566 Details of bonding type rmsd hydrogen bonds : bond 0.09984 ( 630) hydrogen bonds : angle 4.28390 ( 1848) covalent geometry : bond 0.00400 (11104) covalent geometry : angle 0.64021 (15082) *********************** 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 123 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 1.214 Fit side-chains revert: symmetry clash REVERT: A 322 ASN cc_start: 0.7736 (p0) cc_final: 0.7382 (p0) REVERT: A 514 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8557 (tp) REVERT: A 689 ASP cc_start: 0.7743 (m-30) cc_final: 0.7434 (m-30) REVERT: B 24 ASN cc_start: 0.8651 (m-40) cc_final: 0.8393 (m110) REVERT: B 207 GLU cc_start: 0.8087 (pt0) cc_final: 0.7375 (tm-30) REVERT: B 270 LEU cc_start: 0.7809 (tt) cc_final: 0.7570 (tp) REVERT: B 332 ASP cc_start: 0.8121 (t0) cc_final: 0.7365 (m-30) REVERT: B 516 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7419 (mpt180) outliers start: 31 outliers final: 12 residues processed: 110 average time/residue: 1.3301 time to fit residues: 157.7389 Evaluate side-chains 98 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 58 PHE 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 333 VAL Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 516 ARG Chi-restraints excluded: chain B residue 517 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 5 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 B 612 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.134172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.096720 restraints weight = 12107.684| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.89 r_work: 0.3094 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11104 Z= 0.224 Angle : 0.676 9.868 15082 Z= 0.378 Chirality : 0.047 0.160 1800 Planarity : 0.006 0.062 1885 Dihedral : 5.111 55.109 1499 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.63 % Allowed : 11.78 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.22), residues: 1396 helix: 1.73 (0.18), residues: 852 sheet: 3.19 (0.73), residues: 38 loop : -1.54 (0.23), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 63 HIS 0.007 0.002 HIS B 647 PHE 0.021 0.002 PHE B 282 TYR 0.028 0.002 TYR A 9 ARG 0.004 0.001 ARG B 399 Details of bonding type rmsd hydrogen bonds : bond 0.10722 ( 630) hydrogen bonds : angle 4.34512 ( 1848) covalent geometry : bond 0.00477 (11104) covalent geometry : angle 0.67612 (15082) *********************** 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 128 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 1.347 Fit side-chains REVERT: A 322 ASN cc_start: 0.7693 (p0) cc_final: 0.7345 (p0) REVERT: A 514 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8571 (tp) REVERT: A 689 ASP cc_start: 0.7815 (m-30) cc_final: 0.7477 (m-30) REVERT: B 24 ASN cc_start: 0.8732 (m-40) cc_final: 0.8458 (m110) REVERT: B 42 CYS cc_start: 0.4415 (OUTLIER) cc_final: 0.4209 (m) REVERT: B 270 LEU cc_start: 0.7860 (tt) cc_final: 0.7612 (tp) REVERT: B 332 ASP cc_start: 0.8184 (t0) cc_final: 0.7645 (t70) REVERT: B 516 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7410 (mpt180) REVERT: B 579 ARG cc_start: 0.7508 (mtt180) cc_final: 0.7245 (mtt-85) outliers start: 31 outliers final: 16 residues processed: 115 average time/residue: 1.2136 time to fit residues: 151.5352 Evaluate side-chains 111 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 558 ASP 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 42 CYS 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 333 VAL Chi-restraints excluded: chain B residue 389 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 106 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 109 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.136631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.099420 restraints weight = 12101.318| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.86 r_work: 0.3132 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11104 Z= 0.178 Angle : 0.591 9.370 15082 Z= 0.331 Chirality : 0.044 0.157 1800 Planarity : 0.005 0.062 1885 Dihedral : 4.954 52.261 1499 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.20 % Allowed : 12.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.22), residues: 1396 helix: 1.92 (0.18), residues: 856 sheet: 3.20 (0.73), residues: 38 loop : -1.55 (0.23), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 63 HIS 0.005 0.001 HIS B 647 PHE 0.020 0.002 PHE B 282 TYR 0.025 0.002 TYR A 9 ARG 0.002 0.000 ARG B 13 Details of bonding type rmsd hydrogen bonds : bond 0.08929 ( 630) hydrogen bonds : angle 4.18083 ( 1848) covalent geometry : bond 0.00350 (11104) covalent geometry : angle 0.59122 (15082) *********************** 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 119 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 1.228 Fit side-chains REVERT: A 322 ASN cc_start: 0.7716 (p0) cc_final: 0.7360 (p0) REVERT: A 514 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8514 (tp) REVERT: A 580 LYS cc_start: 0.7648 (ttpp) cc_final: 0.7211 (ttpp) REVERT: A 689 ASP cc_start: 0.7765 (m-30) cc_final: 0.7443 (m-30) REVERT: B 24 ASN cc_start: 0.8703 (m-40) cc_final: 0.8397 (m110) REVERT: B 270 LEU cc_start: 0.7812 (tt) cc_final: 0.7565 (tp) REVERT: B 332 ASP cc_start: 0.8166 (t0) cc_final: 0.7360 (m-30) REVERT: B 516 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7374 (mpt180) REVERT: B 579 ARG cc_start: 0.7418 (mtt180) cc_final: 0.7186 (mtt-85) outliers start: 26 outliers final: 11 residues processed: 108 average time/residue: 1.2461 time to fit residues: 145.9962 Evaluate side-chains 102 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 330 THR 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 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 389 ARG Chi-restraints excluded: chain B residue 516 ARG Chi-restraints excluded: chain B residue 517 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 122 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 12 optimal weight: 0.0050 chunk 82 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.7396 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.141159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.104117 restraints weight = 12311.569| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.91 r_work: 0.3200 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11104 Z= 0.133 Angle : 0.505 8.429 15082 Z= 0.282 Chirality : 0.041 0.147 1800 Planarity : 0.005 0.059 1885 Dihedral : 4.615 45.843 1499 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.86 % Allowed : 12.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.22), residues: 1396 helix: 2.28 (0.18), residues: 864 sheet: 3.71 (0.77), residues: 34 loop : -1.42 (0.24), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 63 HIS 0.003 0.001 HIS A 647 PHE 0.017 0.001 PHE A 130 TYR 0.019 0.001 TYR A 9 ARG 0.003 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.06657 ( 630) hydrogen bonds : angle 3.96244 ( 1848) covalent geometry : bond 0.00236 (11104) covalent geometry : angle 0.50495 (15082) *********************** 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 111 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 1.368 Fit side-chains REVERT: A 173 ARG cc_start: 0.6648 (mtm-85) cc_final: 0.5912 (mmm160) REVERT: A 322 ASN cc_start: 0.7711 (p0) cc_final: 0.7377 (p0) REVERT: A 514 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8431 (tp) REVERT: A 580 LYS cc_start: 0.7449 (ttpp) cc_final: 0.7038 (ttpp) REVERT: A 689 ASP cc_start: 0.7799 (m-30) cc_final: 0.7476 (m-30) REVERT: B 24 ASN cc_start: 0.8673 (m-40) cc_final: 0.8352 (m110) REVERT: B 270 LEU cc_start: 0.7776 (tt) cc_final: 0.7534 (tp) REVERT: B 332 ASP cc_start: 0.8090 (t0) cc_final: 0.7328 (m-30) outliers start: 22 outliers final: 12 residues processed: 106 average time/residue: 1.2536 time to fit residues: 144.2575 Evaluate side-chains 91 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 74 LEU 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 514 ILE 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 389 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 52 optimal weight: 0.9980 chunk 4 optimal weight: 0.0970 chunk 107 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 chunk 125 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.139787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.102609 restraints weight = 12329.661| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.89 r_work: 0.3178 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2909 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= 0.141 Angle : 0.521 7.739 15082 Z= 0.289 Chirality : 0.042 0.149 1800 Planarity : 0.005 0.059 1885 Dihedral : 4.505 42.771 1499 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.27 % Allowed : 13.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.22), residues: 1396 helix: 2.32 (0.18), residues: 850 sheet: 3.57 (0.73), residues: 36 loop : -1.32 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 63 HIS 0.004 0.001 HIS A 647 PHE 0.017 0.001 PHE A 130 TYR 0.021 0.001 TYR A 9 ARG 0.003 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.07178 ( 630) hydrogen bonds : angle 3.96529 ( 1848) covalent geometry : bond 0.00257 (11104) covalent geometry : angle 0.52099 (15082) *********************** 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 95 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 1.249 Fit side-chains REVERT: A 173 ARG cc_start: 0.6580 (mtm-85) cc_final: 0.5897 (mmm160) REVERT: A 322 ASN cc_start: 0.7715 (p0) cc_final: 0.7384 (p0) REVERT: A 514 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8439 (tp) REVERT: A 580 LYS cc_start: 0.7426 (ttpp) cc_final: 0.7010 (ttpp) REVERT: A 689 ASP cc_start: 0.7804 (m-30) cc_final: 0.7470 (m-30) REVERT: B 332 ASP cc_start: 0.8095 (t0) cc_final: 0.7344 (m-30) outliers start: 15 outliers final: 12 residues processed: 93 average time/residue: 1.3291 time to fit residues: 133.7002 Evaluate side-chains 90 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 330 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 340 VAL 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 389 ARG 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 79 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 104 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN B 24 ASN B 311 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.138737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.101392 restraints weight = 12159.907| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.91 r_work: 0.3162 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2880 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= 0.151 Angle : 0.541 9.699 15082 Z= 0.300 Chirality : 0.042 0.152 1800 Planarity : 0.005 0.059 1885 Dihedral : 4.469 41.367 1497 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.36 % Allowed : 13.39 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.22), residues: 1396 helix: 2.29 (0.18), residues: 848 sheet: 3.60 (0.73), residues: 36 loop : -1.31 (0.24), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 63 HIS 0.005 0.001 HIS B 647 PHE 0.017 0.001 PHE A 130 TYR 0.022 0.002 TYR A 9 ARG 0.004 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.07693 ( 630) hydrogen bonds : angle 4.00916 ( 1848) covalent geometry : bond 0.00284 (11104) covalent geometry : angle 0.54124 (15082) *********************** 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 97 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 1.484 Fit side-chains REVERT: A 173 ARG cc_start: 0.6701 (mtm-85) cc_final: 0.5967 (mmm160) REVERT: A 322 ASN cc_start: 0.7723 (p0) cc_final: 0.7393 (p0) REVERT: A 514 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8456 (tp) REVERT: A 580 LYS cc_start: 0.7431 (ttpp) cc_final: 0.7014 (ttpp) REVERT: A 689 ASP cc_start: 0.7764 (m-30) cc_final: 0.7451 (m-30) REVERT: B 270 LEU cc_start: 0.7871 (tt) cc_final: 0.7607 (tp) REVERT: B 332 ASP cc_start: 0.8098 (t0) cc_final: 0.7354 (m-30) REVERT: B 516 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7359 (mpt180) outliers start: 16 outliers final: 12 residues processed: 95 average time/residue: 1.4351 time to fit residues: 148.3221 Evaluate side-chains 92 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 75 SER 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 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 389 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 69 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 120 optimal weight: 0.0170 chunk 17 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 15 optimal weight: 7.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.5218 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.142992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.106130 restraints weight = 12427.869| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.91 r_work: 0.3230 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3127 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= 0.119 Angle : 0.480 9.222 15082 Z= 0.263 Chirality : 0.040 0.146 1800 Planarity : 0.004 0.057 1885 Dihedral : 4.250 38.256 1497 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.02 % Allowed : 13.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.23), residues: 1396 helix: 2.51 (0.18), residues: 852 sheet: 3.78 (0.76), residues: 34 loop : -1.27 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 63 HIS 0.003 0.001 HIS B 647 PHE 0.015 0.001 PHE A 130 TYR 0.017 0.001 TYR A 9 ARG 0.002 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.05855 ( 630) hydrogen bonds : angle 3.86399 ( 1848) covalent geometry : bond 0.00207 (11104) covalent geometry : angle 0.47959 (15082) *********************** 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 88 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 1.221 Fit side-chains REVERT: A 173 ARG cc_start: 0.6515 (mtm-85) cc_final: 0.5801 (mmm160) REVERT: A 322 ASN cc_start: 0.7701 (p0) cc_final: 0.7381 (p0) REVERT: A 514 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8471 (tp) REVERT: A 580 LYS cc_start: 0.7324 (ttpp) cc_final: 0.6930 (ttpp) REVERT: A 689 ASP cc_start: 0.7834 (m-30) cc_final: 0.7540 (m-30) REVERT: B 24 ASN cc_start: 0.8679 (m-40) cc_final: 0.8295 (m110) REVERT: B 270 LEU cc_start: 0.7848 (tt) cc_final: 0.7585 (tp) REVERT: B 332 ASP cc_start: 0.8033 (t0) cc_final: 0.7346 (m-30) REVERT: B 516 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7260 (mpt180) outliers start: 12 outliers final: 9 residues processed: 86 average time/residue: 1.2860 time to fit residues: 119.8732 Evaluate side-chains 84 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU 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 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 389 ARG Chi-restraints excluded: chain B residue 516 ARG 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 8 optimal weight: 7.9990 chunk 61 optimal weight: 0.0970 chunk 96 optimal weight: 2.9990 chunk 130 optimal weight: 0.2980 chunk 114 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 50 optimal weight: 0.4980 chunk 107 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3745 r_free = 0.3745 target = 0.140384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.104578 restraints weight = 12184.208| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.95 r_work: 0.3190 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11104 Z= 0.138 Angle : 0.521 9.159 15082 Z= 0.286 Chirality : 0.041 0.146 1800 Planarity : 0.005 0.058 1885 Dihedral : 4.020 24.675 1494 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.10 % Allowed : 14.07 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.23), residues: 1396 helix: 2.46 (0.18), residues: 850 sheet: 3.68 (0.73), residues: 36 loop : -1.22 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 63 HIS 0.004 0.001 HIS B 647 PHE 0.017 0.001 PHE A 130 TYR 0.020 0.001 TYR A 9 ARG 0.003 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.06962 ( 630) hydrogen bonds : angle 3.92102 ( 1848) covalent geometry : bond 0.00257 (11104) covalent geometry : angle 0.52081 (15082) ********************** 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 90 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 1.255 Fit side-chains REVERT: A 173 ARG cc_start: 0.6570 (mtm-85) cc_final: 0.5845 (mmm160) REVERT: A 322 ASN cc_start: 0.7715 (p0) cc_final: 0.7391 (p0) REVERT: A 514 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8428 (tp) REVERT: A 580 LYS cc_start: 0.7343 (ttpp) cc_final: 0.6939 (ttpp) REVERT: A 689 ASP cc_start: 0.7772 (m-30) cc_final: 0.7447 (m-30) REVERT: B 270 LEU cc_start: 0.7837 (tt) cc_final: 0.7592 (tp) REVERT: B 332 ASP cc_start: 0.8025 (t0) cc_final: 0.7313 (m-30) REVERT: B 474 MET cc_start: 0.9119 (tpp) cc_final: 0.8864 (mmp) REVERT: B 516 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7371 (mpt180) outliers start: 13 outliers final: 9 residues processed: 88 average time/residue: 1.2858 time to fit residues: 122.6275 Evaluate side-chains 87 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU 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 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 389 ARG Chi-restraints excluded: chain B residue 516 ARG 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 51 optimal weight: 7.9990 chunk 4 optimal weight: 0.0870 chunk 109 optimal weight: 0.5980 chunk 103 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 79 optimal weight: 0.0010 chunk 62 optimal weight: 2.9990 overall best weight: 0.4966 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.143890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.107168 restraints weight = 12222.558| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.90 r_work: 0.3245 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11104 Z= 0.116 Angle : 0.479 9.247 15082 Z= 0.260 Chirality : 0.040 0.141 1800 Planarity : 0.004 0.056 1885 Dihedral : 3.869 23.996 1494 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.85 % Allowed : 14.32 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.23), residues: 1396 helix: 2.74 (0.18), residues: 838 sheet: 3.80 (0.76), residues: 34 loop : -1.23 (0.24), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 63 HIS 0.003 0.001 HIS B 647 PHE 0.015 0.001 PHE A 130 TYR 0.016 0.001 TYR A 9 ARG 0.002 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.05586 ( 630) hydrogen bonds : angle 3.80848 ( 1848) covalent geometry : bond 0.00206 (11104) covalent geometry : angle 0.47895 (15082) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10042.78 seconds wall clock time: 173 minutes 35.49 seconds (10415.49 seconds total)