Starting phenix.real_space_refine on Mon Jul 28 17:40:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xry_38611/07_2025/8xry_38611.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xry_38611/07_2025/8xry_38611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xry_38611/07_2025/8xry_38611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xry_38611/07_2025/8xry_38611.map" model { file = "/net/cci-nas-00/data/ceres_data/8xry_38611/07_2025/8xry_38611.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xry_38611/07_2025/8xry_38611.cif" } resolution = 3.84 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= 0.008 sd= 0.071 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 36 5.16 5 C 7032 2.51 5 N 1722 2.21 5 O 1826 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10616 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 5308 Classifications: {'peptide': 696} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 31, 'TRANS': 664} Chain breaks: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 167 Restraints were copied for chains: B Time building chain proxies: 10.66, per 1000 atoms: 1.00 Number of scatterers: 10616 At special positions: 0 Unit cell: (90.73, 139.26, 102.335, 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 36 16.00 O 1826 8.00 N 1722 7.00 C 7032 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: 2.87 Conformation dependent library (CDL) restraints added in 1.2 seconds 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2664 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 2 sheets defined 72.0% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 2 through 29 removed outlier: 4.217A pdb=" N ARG A 29 " --> pdb=" O THR A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 32 No H-bonds generated for 'chain 'A' and resid 30 through 32' Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 61 through 67 Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 78 through 100 removed outlier: 3.658A pdb=" N ALA A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 112 removed outlier: 4.395A pdb=" N THR A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Proline residue: A 108 - end of helix Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 134 through 139 removed outlier: 3.567A pdb=" N MET A 139 " --> pdb=" O ASP A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 184 removed outlier: 3.764A pdb=" N GLY A 154 " --> pdb=" O TRP A 150 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ALA A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TRP A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 218 Processing helix chain 'A' and resid 233 through 254 Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 273 through 277 Processing helix chain 'A' and resid 279 through 303 removed outlier: 3.845A pdb=" N TYR A 283 " --> pdb=" O ASP A 279 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 287 " --> pdb=" O TYR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 325 Processing helix chain 'A' and resid 355 through 376 Processing helix chain 'A' and resid 377 through 386 removed outlier: 4.017A pdb=" N ILE A 381 " --> pdb=" O TYR A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 392 through 396 Processing helix chain 'A' and resid 401 through 409 removed outlier: 3.570A pdb=" N ALA A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 439 Proline residue: A 418 - end of helix removed outlier: 4.069A pdb=" N PHE A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) Proline residue: A 430 - end of helix Processing helix chain 'A' and resid 444 through 469 removed outlier: 4.039A pdb=" N ILE A 466 " --> pdb=" O PHE A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 484 Processing helix chain 'A' and resid 486 through 498 removed outlier: 3.690A pdb=" N ILE A 490 " --> pdb=" O LYS A 486 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 501 No H-bonds generated for 'chain 'A' and resid 499 through 501' Processing helix chain 'A' and resid 502 through 523 Processing helix chain 'A' and resid 523 through 536 Processing helix chain 'A' and resid 540 through 546 Processing helix chain 'A' and resid 557 through 572 Processing helix chain 'A' and resid 578 through 601 removed outlier: 3.967A pdb=" N PHE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 610 removed outlier: 4.224A pdb=" N GLY A 610 " --> pdb=" O GLU A 607 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 607 through 610' Processing helix chain 'A' and resid 611 through 638 removed outlier: 4.508A pdb=" N HIS A 615 " --> pdb=" O ARG A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 665 removed outlier: 3.558A pdb=" N VAL A 646 " --> pdb=" O TYR A 642 " (cutoff:3.500A) Proline residue: A 648 - end of helix Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.725A pdb=" N GLU A 669 " --> pdb=" O TYR A 665 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N HIS A 670 " --> pdb=" O GLY A 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 670' Processing helix chain 'A' and resid 686 through 694 removed outlier: 4.105A pdb=" N PHE A 690 " --> pdb=" O LEU A 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 29 removed outlier: 4.217A pdb=" N ARG B 29 " --> pdb=" O THR B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 61 through 67 Processing helix chain 'B' and resid 69 through 77 Processing helix chain 'B' and resid 78 through 100 removed outlier: 3.658A pdb=" N ALA B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 112 removed outlier: 4.394A pdb=" N THR B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 106 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 134 through 139 removed outlier: 3.568A pdb=" N MET B 139 " --> pdb=" O ASP B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 184 removed outlier: 3.764A pdb=" N GLY B 154 " --> pdb=" O TRP B 150 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ALA B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TRP B 158 " --> pdb=" O GLY B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 218 Processing helix chain 'B' and resid 233 through 254 Processing helix chain 'B' and resid 265 through 269 Processing helix chain 'B' and resid 273 through 277 Processing helix chain 'B' and resid 279 through 303 removed outlier: 3.846A pdb=" N TYR B 283 " --> pdb=" O ASP B 279 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B 287 " --> pdb=" O TYR B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 325 Processing helix chain 'B' and resid 355 through 376 Processing helix chain 'B' and resid 377 through 386 removed outlier: 4.018A pdb=" N ILE B 381 " --> pdb=" O TYR B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 391 Processing helix chain 'B' and resid 392 through 396 Processing helix chain 'B' and resid 401 through 409 removed outlier: 3.570A pdb=" N ALA B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 439 Proline residue: B 418 - end of helix removed outlier: 4.070A pdb=" N PHE B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) Proline residue: B 430 - end of helix Processing helix chain 'B' and resid 444 through 469 removed outlier: 4.039A pdb=" N ILE B 466 " --> pdb=" O PHE B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 484 Processing helix chain 'B' and resid 486 through 498 removed outlier: 3.690A pdb=" N ILE B 490 " --> pdb=" O LYS B 486 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 501 No H-bonds generated for 'chain 'B' and resid 499 through 501' Processing helix chain 'B' and resid 502 through 523 Processing helix chain 'B' and resid 523 through 536 Processing helix chain 'B' and resid 540 through 546 Processing helix chain 'B' and resid 557 through 572 Processing helix chain 'B' and resid 578 through 601 removed outlier: 3.967A pdb=" N PHE B 582 " --> pdb=" O LEU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 610 removed outlier: 4.224A pdb=" N GLY B 610 " --> pdb=" O GLU B 607 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 607 through 610' Processing helix chain 'B' and resid 611 through 638 removed outlier: 4.509A pdb=" N HIS B 615 " --> pdb=" O ARG B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 665 removed outlier: 3.558A pdb=" N VAL B 646 " --> pdb=" O TYR B 642 " (cutoff:3.500A) Proline residue: B 648 - end of helix Processing helix chain 'B' and resid 665 through 670 removed outlier: 3.726A pdb=" N GLU B 669 " --> pdb=" O TYR B 665 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N HIS B 670 " --> pdb=" O GLY B 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 665 through 670' Processing helix chain 'B' and resid 686 through 694 removed outlier: 4.105A pdb=" N PHE B 690 " --> pdb=" O LEU B 686 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 228 through 229 Processing sheet with id=AA2, first strand: chain 'B' and resid 228 through 229 672 hydrogen bonds defined for protein. 1944 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: 3.31 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3211 1.34 - 1.46: 2241 1.46 - 1.58: 5382 1.58 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 10892 Sorted by residual: bond pdb=" C LEU B 498 " pdb=" N PRO B 499 " ideal model delta sigma weight residual 1.334 1.348 -0.014 8.40e-03 1.42e+04 2.87e+00 bond pdb=" C LEU A 498 " pdb=" N PRO A 499 " ideal model delta sigma weight residual 1.334 1.347 -0.013 8.40e-03 1.42e+04 2.52e+00 bond pdb=" C ILE B 397 " pdb=" N PRO B 398 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.22e+00 bond pdb=" C ILE A 397 " pdb=" N PRO A 398 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.17e+00 bond pdb=" CA GLN A 206 " pdb=" C GLN A 206 " ideal model delta sigma weight residual 1.523 1.535 -0.012 1.34e-02 5.57e+03 8.41e-01 ... (remaining 10887 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 14549 2.11 - 4.22: 247 4.22 - 6.33: 58 6.33 - 8.45: 8 8.45 - 10.56: 6 Bond angle restraints: 14868 Sorted by residual: angle pdb=" C PRO A 203 " pdb=" N ASP A 204 " pdb=" CA ASP A 204 " ideal model delta sigma weight residual 121.54 128.50 -6.96 1.91e+00 2.74e-01 1.33e+01 angle pdb=" C PRO B 203 " pdb=" N ASP B 204 " pdb=" CA ASP B 204 " ideal model delta sigma weight residual 121.54 128.47 -6.93 1.91e+00 2.74e-01 1.32e+01 angle pdb=" C PRO A 58 " pdb=" N PHE A 59 " pdb=" CA PHE A 59 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.27e+01 angle pdb=" C PRO B 58 " pdb=" N PHE B 59 " pdb=" CA PHE B 59 " ideal model delta sigma weight residual 121.54 128.29 -6.75 1.91e+00 2.74e-01 1.25e+01 angle pdb=" C LYS B 486 " pdb=" N LEU B 487 " pdb=" CA LEU B 487 " ideal model delta sigma weight residual 121.54 127.64 -6.10 1.91e+00 2.74e-01 1.02e+01 ... (remaining 14863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.33: 5710 16.33 - 32.66: 558 32.66 - 48.98: 90 48.98 - 65.31: 16 65.31 - 81.64: 2 Dihedral angle restraints: 6376 sinusoidal: 2270 harmonic: 4106 Sorted by residual: dihedral pdb=" CA PHE A 59 " pdb=" C PHE A 59 " pdb=" N ALA A 60 " pdb=" CA ALA A 60 " ideal model delta harmonic sigma weight residual 180.00 146.92 33.08 0 5.00e+00 4.00e-02 4.38e+01 dihedral pdb=" CA PHE B 59 " pdb=" C PHE B 59 " pdb=" N ALA B 60 " pdb=" CA ALA B 60 " ideal model delta harmonic sigma weight residual 180.00 146.95 33.05 0 5.00e+00 4.00e-02 4.37e+01 dihedral pdb=" CA GLY B 441 " pdb=" C GLY B 441 " pdb=" N ILE B 442 " pdb=" CA ILE B 442 " ideal model delta harmonic sigma weight residual 180.00 151.20 28.80 0 5.00e+00 4.00e-02 3.32e+01 ... (remaining 6373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1162 0.037 - 0.074: 441 0.074 - 0.111: 140 0.111 - 0.148: 27 0.148 - 0.185: 6 Chirality restraints: 1776 Sorted by residual: chirality pdb=" CA ASP A 204 " pdb=" N ASP A 204 " pdb=" C ASP A 204 " pdb=" CB ASP A 204 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.55e-01 chirality pdb=" CA ASP B 204 " pdb=" N ASP B 204 " pdb=" C ASP B 204 " pdb=" CB ASP B 204 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.07e-01 chirality pdb=" CA PHE A 664 " pdb=" N PHE A 664 " pdb=" C PHE A 664 " pdb=" CB PHE A 664 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.15e-01 ... (remaining 1773 not shown) Planarity restraints: 1826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 202 " 0.046 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO A 203 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 203 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 203 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 202 " -0.046 5.00e-02 4.00e+02 6.97e-02 7.77e+00 pdb=" N PRO B 203 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 203 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 203 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 484 " 0.046 5.00e-02 4.00e+02 6.89e-02 7.60e+00 pdb=" N PRO A 485 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 485 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 485 " 0.038 5.00e-02 4.00e+02 ... (remaining 1823 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2534 2.78 - 3.31: 10899 3.31 - 3.84: 17498 3.84 - 4.37: 18819 4.37 - 4.90: 32469 Nonbonded interactions: 82219 Sorted by model distance: nonbonded pdb=" NH2 ARG A 56 " pdb=" O ALA A 60 " model vdw 2.253 3.120 nonbonded pdb=" NH2 ARG B 56 " pdb=" O ALA B 60 " model vdw 2.254 3.120 nonbonded pdb=" ND2 ASN A 261 " pdb=" OG SER A 280 " model vdw 2.299 3.120 nonbonded pdb=" OD1 ASP A 562 " pdb=" OH TYR A 586 " model vdw 2.299 3.040 nonbonded pdb=" OD1 ASP B 562 " pdb=" OH TYR B 586 " model vdw 2.300 3.040 ... (remaining 82214 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 31.850 Find NCS groups from input model: 0.210 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: 0.000 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10892 Z= 0.165 Angle : 0.744 10.558 14868 Z= 0.395 Chirality : 0.044 0.185 1776 Planarity : 0.005 0.070 1826 Dihedral : 12.985 81.641 3712 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.32 % Favored : 90.53 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.26 (0.24), residues: 1384 helix: 0.98 (0.18), residues: 904 sheet: None (None), residues: 0 loop : -2.50 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 613 HIS 0.005 0.001 HIS A 615 PHE 0.018 0.002 PHE B 376 TYR 0.024 0.002 TYR B 171 ARG 0.002 0.000 ARG A 359 Details of bonding type rmsd hydrogen bonds : bond 0.13394 ( 672) hydrogen bonds : angle 5.16342 ( 1944) covalent geometry : bond 0.00350 (10892) covalent geometry : angle 0.74391 (14868) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 1.131 Fit side-chains REVERT: A 240 TRP cc_start: 0.9092 (t60) cc_final: 0.8641 (t60) REVERT: A 462 PHE cc_start: 0.7374 (m-10) cc_final: 0.7127 (m-10) REVERT: A 522 SER cc_start: 0.9371 (p) cc_final: 0.9118 (p) REVERT: B 14 PHE cc_start: 0.8836 (t80) cc_final: 0.8592 (t80) REVERT: B 26 TRP cc_start: 0.8555 (t60) cc_final: 0.8331 (t60) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1690 time to fit residues: 46.1162 Evaluate side-chains 139 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 108 optimal weight: 30.0000 chunk 41 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 125 optimal weight: 0.3980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 353 ASN B 261 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.163682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.123221 restraints weight = 14898.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.121941 restraints weight = 22059.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.123464 restraints weight = 20635.617| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10892 Z= 0.163 Angle : 0.697 12.060 14868 Z= 0.348 Chirality : 0.043 0.167 1776 Planarity : 0.005 0.063 1826 Dihedral : 5.239 32.015 1484 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.45 % Favored : 91.40 % Rotamer: Outliers : 1.96 % Allowed : 10.34 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -0.26 (0.24), residues: 1384 helix: 1.02 (0.18), residues: 912 sheet: None (None), residues: 0 loop : -2.67 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 613 HIS 0.004 0.001 HIS A 615 PHE 0.037 0.002 PHE B 640 TYR 0.016 0.002 TYR B 171 ARG 0.002 0.000 ARG B 450 Details of bonding type rmsd hydrogen bonds : bond 0.04568 ( 672) hydrogen bonds : angle 4.43377 ( 1944) covalent geometry : bond 0.00377 (10892) covalent geometry : angle 0.69695 (14868) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 3.268 Fit side-chains REVERT: A 113 ASP cc_start: 0.7652 (p0) cc_final: 0.7254 (p0) REVERT: A 198 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7599 (m-30) REVERT: A 240 TRP cc_start: 0.9057 (t60) cc_final: 0.8668 (t60) REVERT: A 519 LEU cc_start: 0.9403 (mm) cc_final: 0.9130 (mp) REVERT: A 522 SER cc_start: 0.9312 (p) cc_final: 0.9041 (p) REVERT: A 642 TYR cc_start: 0.6774 (p90) cc_final: 0.6335 (p90) REVERT: B 14 PHE cc_start: 0.8771 (t80) cc_final: 0.8543 (t80) REVERT: B 113 ASP cc_start: 0.7534 (p0) cc_final: 0.7206 (p0) REVERT: B 522 SER cc_start: 0.9397 (p) cc_final: 0.9182 (p) REVERT: B 690 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.7273 (m-10) outliers start: 21 outliers final: 14 residues processed: 174 average time/residue: 0.2095 time to fit residues: 59.4983 Evaluate side-chains 159 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 690 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 44 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 chunk 113 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 67 optimal weight: 0.0060 chunk 34 optimal weight: 0.9990 chunk 123 optimal weight: 0.1980 chunk 41 optimal weight: 0.0050 chunk 79 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 overall best weight: 0.2210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.171760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.124852 restraints weight = 15102.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.126717 restraints weight = 11158.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.127637 restraints weight = 9339.916| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10892 Z= 0.116 Angle : 0.639 10.713 14868 Z= 0.314 Chirality : 0.041 0.130 1776 Planarity : 0.005 0.063 1826 Dihedral : 4.973 31.541 1484 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 2.33 % Allowed : 14.43 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.14 (0.24), residues: 1384 helix: 1.10 (0.18), residues: 914 sheet: -2.05 (1.16), residues: 20 loop : -2.60 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 61 HIS 0.005 0.001 HIS A 615 PHE 0.028 0.001 PHE B 513 TYR 0.024 0.001 TYR B 171 ARG 0.002 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.03725 ( 672) hydrogen bonds : angle 4.17346 ( 1944) covalent geometry : bond 0.00244 (10892) covalent geometry : angle 0.63929 (14868) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 1.225 Fit side-chains revert: symmetry clash REVERT: A 102 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7939 (tp) REVERT: A 113 ASP cc_start: 0.7500 (p0) cc_final: 0.7063 (p0) REVERT: A 240 TRP cc_start: 0.8997 (t60) cc_final: 0.8492 (t60) REVERT: A 519 LEU cc_start: 0.9465 (mm) cc_final: 0.9226 (mp) REVERT: A 642 TYR cc_start: 0.6659 (p90) cc_final: 0.6366 (p90) REVERT: B 14 PHE cc_start: 0.8863 (t80) cc_final: 0.8627 (t80) REVERT: B 102 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8145 (tp) REVERT: B 113 ASP cc_start: 0.7604 (p0) cc_final: 0.7132 (p0) REVERT: B 571 CYS cc_start: 0.7685 (m) cc_final: 0.7430 (t) REVERT: B 690 PHE cc_start: 0.7577 (OUTLIER) cc_final: 0.7078 (m-10) outliers start: 25 outliers final: 13 residues processed: 191 average time/residue: 0.2899 time to fit residues: 84.7276 Evaluate side-chains 162 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 690 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 47 optimal weight: 50.0000 chunk 119 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 chunk 40 optimal weight: 20.0000 chunk 44 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN B 261 ASN B 670 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.166696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.119672 restraints weight = 14964.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.120434 restraints weight = 10950.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.120633 restraints weight = 9783.428| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10892 Z= 0.177 Angle : 0.664 10.485 14868 Z= 0.328 Chirality : 0.043 0.177 1776 Planarity : 0.005 0.064 1826 Dihedral : 4.935 30.978 1484 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 3.45 % Allowed : 17.69 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -0.13 (0.24), residues: 1384 helix: 1.11 (0.18), residues: 918 sheet: -1.78 (1.20), residues: 20 loop : -2.63 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 613 HIS 0.002 0.001 HIS A 615 PHE 0.028 0.001 PHE A 513 TYR 0.036 0.002 TYR B 171 ARG 0.008 0.000 ARG B 619 Details of bonding type rmsd hydrogen bonds : bond 0.03920 ( 672) hydrogen bonds : angle 4.15558 ( 1944) covalent geometry : bond 0.00418 (10892) covalent geometry : angle 0.66400 (14868) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 ASP cc_start: 0.7687 (p0) cc_final: 0.7220 (p0) REVERT: A 226 ARG cc_start: 0.6016 (ptm160) cc_final: 0.5762 (ptm160) REVERT: A 240 TRP cc_start: 0.8971 (t60) cc_final: 0.8440 (t60) REVERT: A 548 TRP cc_start: 0.8597 (p-90) cc_final: 0.8209 (p-90) REVERT: A 642 TYR cc_start: 0.6633 (p90) cc_final: 0.6352 (p90) REVERT: B 14 PHE cc_start: 0.8864 (t80) cc_final: 0.8653 (t80) REVERT: B 29 ARG cc_start: 0.7843 (mtm-85) cc_final: 0.7601 (mtt180) outliers start: 37 outliers final: 25 residues processed: 170 average time/residue: 0.1937 time to fit residues: 50.7012 Evaluate side-chains 154 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 690 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 129 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 88 optimal weight: 0.2980 chunk 125 optimal weight: 1.9990 chunk 132 optimal weight: 0.0980 chunk 104 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 670 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.164875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.120868 restraints weight = 14927.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.120493 restraints weight = 17635.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.121917 restraints weight = 14448.024| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10892 Z= 0.121 Angle : 0.657 12.557 14868 Z= 0.314 Chirality : 0.041 0.163 1776 Planarity : 0.005 0.065 1826 Dihedral : 4.803 31.528 1484 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.89 % Allowed : 19.37 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -0.02 (0.24), residues: 1384 helix: 1.17 (0.18), residues: 916 sheet: -1.17 (1.31), residues: 20 loop : -2.56 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 613 HIS 0.002 0.000 HIS A 615 PHE 0.028 0.001 PHE A 513 TYR 0.033 0.001 TYR B 171 ARG 0.004 0.000 ARG B 619 Details of bonding type rmsd hydrogen bonds : bond 0.03635 ( 672) hydrogen bonds : angle 4.05798 ( 1944) covalent geometry : bond 0.00271 (10892) covalent geometry : angle 0.65658 (14868) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.8007 (mtm-85) cc_final: 0.7770 (mtt-85) REVERT: A 113 ASP cc_start: 0.7453 (p0) cc_final: 0.7070 (p0) REVERT: A 240 TRP cc_start: 0.8985 (t60) cc_final: 0.8451 (t60) REVERT: A 519 LEU cc_start: 0.9484 (mm) cc_final: 0.9228 (mp) REVERT: A 642 TYR cc_start: 0.6554 (p90) cc_final: 0.6282 (p90) REVERT: B 14 PHE cc_start: 0.8803 (t80) cc_final: 0.8588 (t80) REVERT: B 520 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8522 (tm-30) REVERT: B 521 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9001 (tt) outliers start: 31 outliers final: 23 residues processed: 168 average time/residue: 0.2191 time to fit residues: 54.6086 Evaluate side-chains 163 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 690 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 38 optimal weight: 10.0000 chunk 66 optimal weight: 0.0070 chunk 90 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 109 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 chunk 108 optimal weight: 30.0000 chunk 15 optimal weight: 0.5980 overall best weight: 0.8402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.166463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.121994 restraints weight = 15031.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.123005 restraints weight = 16299.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.124191 restraints weight = 11795.327| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10892 Z= 0.137 Angle : 0.659 11.379 14868 Z= 0.314 Chirality : 0.041 0.163 1776 Planarity : 0.005 0.068 1826 Dihedral : 4.733 31.281 1484 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 4.19 % Allowed : 19.18 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.04 (0.24), residues: 1384 helix: 1.17 (0.18), residues: 918 sheet: -0.94 (1.34), residues: 20 loop : -2.46 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 548 HIS 0.002 0.000 HIS A 615 PHE 0.025 0.001 PHE A 513 TYR 0.036 0.001 TYR B 171 ARG 0.004 0.000 ARG B 619 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 672) hydrogen bonds : angle 4.02596 ( 1944) covalent geometry : bond 0.00321 (10892) covalent geometry : angle 0.65903 (14868) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 145 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7320 (ttm110) cc_final: 0.7047 (ttm110) REVERT: A 113 ASP cc_start: 0.7404 (p0) cc_final: 0.7069 (p0) REVERT: A 240 TRP cc_start: 0.8986 (t60) cc_final: 0.8431 (t60) REVERT: A 519 LEU cc_start: 0.9517 (mm) cc_final: 0.9152 (mp) REVERT: A 642 TYR cc_start: 0.6629 (p90) cc_final: 0.6358 (p90) REVERT: B 14 PHE cc_start: 0.8758 (t80) cc_final: 0.8551 (t80) REVERT: B 520 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8528 (tm-30) REVERT: B 521 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9110 (tt) REVERT: B 522 SER cc_start: 0.9322 (p) cc_final: 0.9098 (p) outliers start: 45 outliers final: 35 residues processed: 177 average time/residue: 0.2099 time to fit residues: 56.5590 Evaluate side-chains 176 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 690 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 111 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.158257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.114442 restraints weight = 15446.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.112710 restraints weight = 19158.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.114115 restraints weight = 18459.661| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10892 Z= 0.142 Angle : 0.661 13.055 14868 Z= 0.314 Chirality : 0.042 0.161 1776 Planarity : 0.005 0.072 1826 Dihedral : 4.705 31.191 1484 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.82 % Allowed : 20.20 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.15 (0.25), residues: 1384 helix: 1.23 (0.18), residues: 924 sheet: -0.85 (1.33), residues: 20 loop : -2.39 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 548 HIS 0.003 0.001 HIS A 615 PHE 0.024 0.001 PHE A 513 TYR 0.037 0.001 TYR B 171 ARG 0.003 0.000 ARG B 619 Details of bonding type rmsd hydrogen bonds : bond 0.03594 ( 672) hydrogen bonds : angle 3.99994 ( 1944) covalent geometry : bond 0.00335 (10892) covalent geometry : angle 0.66057 (14868) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 144 time to evaluate : 1.807 Fit side-chains REVERT: A 63 ARG cc_start: 0.7374 (ttm110) cc_final: 0.7107 (ttm110) REVERT: A 113 ASP cc_start: 0.7422 (p0) cc_final: 0.7108 (p0) REVERT: A 519 LEU cc_start: 0.9513 (mm) cc_final: 0.9165 (mp) REVERT: A 548 TRP cc_start: 0.8877 (p-90) cc_final: 0.8629 (p-90) REVERT: A 642 TYR cc_start: 0.6607 (p90) cc_final: 0.6335 (p90) REVERT: B 14 PHE cc_start: 0.8780 (t80) cc_final: 0.8563 (t80) REVERT: B 378 MET cc_start: 0.6945 (mmm) cc_final: 0.6707 (mmm) REVERT: B 520 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8557 (tm-30) REVERT: B 521 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9119 (tt) REVERT: B 690 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.7249 (m-10) outliers start: 41 outliers final: 31 residues processed: 171 average time/residue: 0.2612 time to fit residues: 69.0555 Evaluate side-chains 176 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 690 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 58 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 69 optimal weight: 20.0000 chunk 50 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.163806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.114210 restraints weight = 16108.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.112024 restraints weight = 14571.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.113690 restraints weight = 12596.278| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10892 Z= 0.155 Angle : 0.676 13.006 14868 Z= 0.321 Chirality : 0.042 0.160 1776 Planarity : 0.005 0.075 1826 Dihedral : 4.709 31.990 1484 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 3.63 % Allowed : 20.76 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.15 (0.25), residues: 1384 helix: 1.22 (0.18), residues: 928 sheet: -0.77 (1.33), residues: 20 loop : -2.39 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 548 HIS 0.003 0.001 HIS A 615 PHE 0.019 0.001 PHE B 690 TYR 0.038 0.001 TYR B 171 ARG 0.005 0.000 ARG B 56 Details of bonding type rmsd hydrogen bonds : bond 0.03656 ( 672) hydrogen bonds : angle 4.00663 ( 1944) covalent geometry : bond 0.00370 (10892) covalent geometry : angle 0.67579 (14868) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 1.134 Fit side-chains REVERT: A 63 ARG cc_start: 0.7418 (ttm110) cc_final: 0.7136 (ttm110) REVERT: A 113 ASP cc_start: 0.7763 (p0) cc_final: 0.7397 (p0) REVERT: A 378 MET cc_start: 0.7519 (mmm) cc_final: 0.6654 (mtp) REVERT: A 519 LEU cc_start: 0.9534 (mm) cc_final: 0.9177 (mp) REVERT: A 642 TYR cc_start: 0.6498 (p90) cc_final: 0.6221 (p90) REVERT: B 14 PHE cc_start: 0.8817 (t80) cc_final: 0.8610 (t80) REVERT: B 378 MET cc_start: 0.7327 (mmm) cc_final: 0.6943 (mmm) REVERT: B 520 GLU cc_start: 0.8941 (tm-30) cc_final: 0.8715 (tm-30) REVERT: B 521 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9124 (tt) outliers start: 39 outliers final: 32 residues processed: 168 average time/residue: 0.1722 time to fit residues: 44.3005 Evaluate side-chains 168 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 690 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 95 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 33 optimal weight: 0.0470 chunk 79 optimal weight: 1.9990 chunk 122 optimal weight: 0.0670 chunk 27 optimal weight: 0.8980 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.164025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.114191 restraints weight = 16269.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.111559 restraints weight = 12340.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.111462 restraints weight = 11351.556| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10892 Z= 0.135 Angle : 0.669 13.661 14868 Z= 0.316 Chirality : 0.041 0.159 1776 Planarity : 0.005 0.077 1826 Dihedral : 4.664 31.563 1484 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 3.54 % Allowed : 20.58 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.22 (0.25), residues: 1384 helix: 1.35 (0.18), residues: 916 sheet: -0.70 (1.34), residues: 20 loop : -2.45 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 548 HIS 0.002 0.000 HIS A 615 PHE 0.019 0.001 PHE B 690 TYR 0.036 0.001 TYR B 171 ARG 0.004 0.000 ARG B 56 Details of bonding type rmsd hydrogen bonds : bond 0.03557 ( 672) hydrogen bonds : angle 3.97804 ( 1944) covalent geometry : bond 0.00316 (10892) covalent geometry : angle 0.66876 (14868) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 1.093 Fit side-chains REVERT: A 63 ARG cc_start: 0.7369 (ttm110) cc_final: 0.7092 (ttm110) REVERT: A 113 ASP cc_start: 0.7814 (p0) cc_final: 0.7423 (p0) REVERT: A 232 GLU cc_start: 0.6404 (pm20) cc_final: 0.6191 (pm20) REVERT: A 378 MET cc_start: 0.7655 (mmm) cc_final: 0.6705 (mtp) REVERT: A 519 LEU cc_start: 0.9523 (mm) cc_final: 0.9167 (mp) REVERT: A 642 TYR cc_start: 0.6488 (p90) cc_final: 0.6217 (p90) REVERT: A 661 ARG cc_start: 0.8233 (ttm-80) cc_final: 0.7985 (ttm-80) REVERT: B 378 MET cc_start: 0.7442 (mmm) cc_final: 0.7077 (mmm) REVERT: B 520 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8707 (tm-30) REVERT: B 521 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9044 (tt) outliers start: 38 outliers final: 33 residues processed: 168 average time/residue: 0.1861 time to fit residues: 47.3176 Evaluate side-chains 173 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 690 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 135 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 89 optimal weight: 0.0370 chunk 95 optimal weight: 0.0040 chunk 50 optimal weight: 5.9990 chunk 72 optimal weight: 0.1980 chunk 85 optimal weight: 1.9990 chunk 106 optimal weight: 0.0970 chunk 131 optimal weight: 0.8980 overall best weight: 0.2068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.168029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.117788 restraints weight = 16217.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.116880 restraints weight = 11365.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.116853 restraints weight = 10219.919| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10892 Z= 0.110 Angle : 0.654 14.429 14868 Z= 0.306 Chirality : 0.040 0.160 1776 Planarity : 0.005 0.079 1826 Dihedral : 4.500 31.169 1484 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 2.33 % Allowed : 22.35 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.43 (0.25), residues: 1384 helix: 1.45 (0.18), residues: 918 sheet: -0.13 (1.41), residues: 20 loop : -2.26 (0.32), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 548 HIS 0.001 0.000 HIS A 173 PHE 0.019 0.001 PHE B 664 TYR 0.024 0.001 TYR B 171 ARG 0.003 0.000 ARG B 56 Details of bonding type rmsd hydrogen bonds : bond 0.03198 ( 672) hydrogen bonds : angle 3.90383 ( 1944) covalent geometry : bond 0.00239 (10892) covalent geometry : angle 0.65415 (14868) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 1.163 Fit side-chains REVERT: A 63 ARG cc_start: 0.7360 (ttm110) cc_final: 0.7049 (ttm110) REVERT: A 113 ASP cc_start: 0.7717 (p0) cc_final: 0.7342 (p0) REVERT: A 378 MET cc_start: 0.7469 (mmm) cc_final: 0.6338 (mtt) REVERT: A 519 LEU cc_start: 0.9504 (mm) cc_final: 0.9167 (mp) REVERT: A 548 TRP cc_start: 0.8933 (p-90) cc_final: 0.8649 (p-90) REVERT: A 571 CYS cc_start: 0.7934 (m) cc_final: 0.7159 (t) REVERT: A 642 TYR cc_start: 0.6408 (p90) cc_final: 0.6133 (p90) REVERT: B 183 MET cc_start: 0.7894 (tpp) cc_final: 0.7646 (tpp) REVERT: B 378 MET cc_start: 0.7401 (mmm) cc_final: 0.6973 (mmm) REVERT: B 571 CYS cc_start: 0.7930 (m) cc_final: 0.7540 (t) REVERT: B 690 PHE cc_start: 0.7660 (OUTLIER) cc_final: 0.7406 (m-10) outliers start: 25 outliers final: 17 residues processed: 165 average time/residue: 0.1972 time to fit residues: 49.4983 Evaluate side-chains 153 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 690 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 93 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 37 optimal weight: 0.0770 chunk 40 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 74 optimal weight: 0.0060 chunk 78 optimal weight: 2.9990 chunk 121 optimal weight: 0.0010 overall best weight: 0.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.166585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.117523 restraints weight = 16243.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.115281 restraints weight = 14317.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.116288 restraints weight = 12292.331| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10892 Z= 0.123 Angle : 0.663 14.146 14868 Z= 0.314 Chirality : 0.041 0.160 1776 Planarity : 0.005 0.080 1826 Dihedral : 4.470 32.330 1484 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 2.14 % Allowed : 22.16 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.45 (0.25), residues: 1384 helix: 1.49 (0.18), residues: 918 sheet: -0.64 (1.33), residues: 22 loop : -2.30 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 548 HIS 0.002 0.000 HIS A 615 PHE 0.031 0.001 PHE B 664 TYR 0.020 0.001 TYR B 171 ARG 0.003 0.000 ARG B 619 Details of bonding type rmsd hydrogen bonds : bond 0.03301 ( 672) hydrogen bonds : angle 3.90661 ( 1944) covalent geometry : bond 0.00283 (10892) covalent geometry : angle 0.66251 (14868) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3650.19 seconds wall clock time: 68 minutes 29.71 seconds (4109.71 seconds total)