Starting phenix.real_space_refine on Wed Mar 4 00:50:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jpf_6822/03_2026/6jpf_6822.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jpf_6822/03_2026/6jpf_6822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6jpf_6822/03_2026/6jpf_6822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jpf_6822/03_2026/6jpf_6822.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6jpf_6822/03_2026/6jpf_6822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jpf_6822/03_2026/6jpf_6822.map" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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 42 5.16 5 C 6368 2.51 5 N 1572 2.21 5 O 1606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9588 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4794 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 32, 'TRANS': 577} Chain breaks: 6 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 8, 'ASN:plan1': 4, 'ASP:plan': 4, 'TYR:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 90 Restraints were copied for chains: B Time building chain proxies: 3.34, per 1000 atoms: 0.35 Number of scatterers: 9588 At special positions: 0 Unit cell: (119, 131, 91, 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 42 16.00 O 1606 8.00 N 1572 7.00 C 6368 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 376.2 milliseconds 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2340 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 4 sheets defined 75.5% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 4 through 31 Processing helix chain 'A' and resid 34 through 39 removed outlier: 3.605A pdb=" N TYR A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 75 through 81 removed outlier: 3.755A pdb=" N LEU A 80 " --> pdb=" O MET A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 118 removed outlier: 7.485A pdb=" N LEU A 93 " --> pdb=" O ASP A 89 " (cutoff:3.500A) removed outlier: 9.706A pdb=" N ASP A 94 " --> pdb=" O HIS A 90 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 157 through 195 removed outlier: 3.793A pdb=" N ILE A 164 " --> pdb=" O TRP A 160 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N MET A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 202 removed outlier: 3.743A pdb=" N PHE A 202 " --> pdb=" O ARG A 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 202' Processing helix chain 'A' and resid 216 through 229 Processing helix chain 'A' and resid 242 through 267 removed outlier: 3.660A pdb=" N TYR A 262 " --> pdb=" O TRP A 258 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N THR A 267 " --> pdb=" O GLN A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 314 Processing helix chain 'A' and resid 330 through 340 Processing helix chain 'A' and resid 361 through 365 Processing helix chain 'A' and resid 372 through 388 Processing helix chain 'A' and resid 390 through 402 removed outlier: 3.542A pdb=" N ILE A 394 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 439 removed outlier: 3.953A pdb=" N GLY A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 453 Processing helix chain 'A' and resid 457 through 476 removed outlier: 3.625A pdb=" N VAL A 475 " --> pdb=" O ILE A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 491 removed outlier: 3.769A pdb=" N GLN A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A 491 " --> pdb=" O ALA A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 524 removed outlier: 3.671A pdb=" N THR A 515 " --> pdb=" O PRO A 511 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE A 516 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 535 removed outlier: 4.012A pdb=" N LEU A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 548 Processing helix chain 'A' and resid 566 through 585 Proline residue: A 572 - end of helix Processing helix chain 'A' and resid 591 through 613 Processing helix chain 'A' and resid 624 through 648 removed outlier: 3.651A pdb=" N THR A 634 " --> pdb=" O GLY A 630 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY A 645 " --> pdb=" O LEU A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 682 removed outlier: 4.545A pdb=" N PHE A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) Proline residue: A 663 - end of helix Proline residue: A 679 - end of helix Processing helix chain 'A' and resid 685 through 700 Processing helix chain 'A' and resid 704 through 713 removed outlier: 4.386A pdb=" N TYR A 708 " --> pdb=" O ASN A 704 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR A 713 " --> pdb=" O LEU A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 31 Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.606A pdb=" N TYR B 38 " --> pdb=" O ASN B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 75 through 81 removed outlier: 3.755A pdb=" N LEU B 80 " --> pdb=" O MET B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 118 removed outlier: 7.485A pdb=" N LEU B 93 " --> pdb=" O ASP B 89 " (cutoff:3.500A) removed outlier: 9.706A pdb=" N ASP B 94 " --> pdb=" O HIS B 90 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 157 through 195 removed outlier: 3.792A pdb=" N ILE B 164 " --> pdb=" O TRP B 160 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N MET B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 202 removed outlier: 3.744A pdb=" N PHE B 202 " --> pdb=" O ARG B 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 202' Processing helix chain 'B' and resid 216 through 229 Processing helix chain 'B' and resid 242 through 267 removed outlier: 3.659A pdb=" N TYR B 262 " --> pdb=" O TRP B 258 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N THR B 267 " --> pdb=" O GLN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 314 Processing helix chain 'B' and resid 330 through 340 Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 372 through 388 Processing helix chain 'B' and resid 390 through 402 removed outlier: 3.542A pdb=" N ILE B 394 " --> pdb=" O PHE B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 439 removed outlier: 3.952A pdb=" N GLY B 432 " --> pdb=" O GLY B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 453 Processing helix chain 'B' and resid 457 through 476 removed outlier: 3.626A pdb=" N VAL B 475 " --> pdb=" O ILE B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 491 removed outlier: 3.768A pdb=" N GLN B 490 " --> pdb=" O ALA B 486 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 524 removed outlier: 3.672A pdb=" N THR B 515 " --> pdb=" O PRO B 511 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE B 516 " --> pdb=" O MET B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 535 removed outlier: 4.012A pdb=" N LEU B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 548 Processing helix chain 'B' and resid 566 through 585 Proline residue: B 572 - end of helix Processing helix chain 'B' and resid 591 through 613 Processing helix chain 'B' and resid 624 through 648 removed outlier: 3.651A pdb=" N THR B 634 " --> pdb=" O GLY B 630 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY B 645 " --> pdb=" O LEU B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 682 removed outlier: 4.546A pdb=" N PHE B 658 " --> pdb=" O SER B 654 " (cutoff:3.500A) Proline residue: B 663 - end of helix Proline residue: B 679 - end of helix Processing helix chain 'B' and resid 685 through 700 Processing helix chain 'B' and resid 704 through 713 removed outlier: 4.387A pdb=" N TYR B 708 " --> pdb=" O ASN B 704 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR B 713 " --> pdb=" O LEU B 709 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 235 removed outlier: 5.686A pdb=" N ALA A 323 " --> pdb=" O VAL A 239 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 233 through 235 Processing sheet with id=AA3, first strand: chain 'B' and resid 233 through 235 removed outlier: 5.686A pdb=" N ALA B 323 " --> pdb=" O VAL B 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 233 through 235 659 hydrogen bonds defined for protein. 1959 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.50 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2922 1.34 - 1.46: 2236 1.46 - 1.58: 4620 1.58 - 1.70: 0 1.70 - 1.81: 76 Bond restraints: 9854 Sorted by residual: bond pdb=" CB THR A 173 " pdb=" CG2 THR A 173 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.03e+00 bond pdb=" CB THR B 173 " pdb=" CG2 THR B 173 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 3.99e+00 bond pdb=" CZ ARG B 29 " pdb=" NH2 ARG B 29 " ideal model delta sigma weight residual 1.330 1.307 0.023 1.30e-02 5.92e+03 3.17e+00 bond pdb=" CZ ARG A 29 " pdb=" NH2 ARG A 29 " ideal model delta sigma weight residual 1.330 1.307 0.023 1.30e-02 5.92e+03 3.15e+00 bond pdb=" N ILE B 714 " pdb=" CA ILE B 714 " ideal model delta sigma weight residual 1.459 1.438 0.021 1.25e-02 6.40e+03 2.89e+00 ... (remaining 9849 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 12938 1.64 - 3.28: 389 3.28 - 4.92: 75 4.92 - 6.57: 27 6.57 - 8.21: 9 Bond angle restraints: 13438 Sorted by residual: angle pdb=" N PRO B 275 " pdb=" CA PRO B 275 " pdb=" CB PRO B 275 " ideal model delta sigma weight residual 103.00 110.45 -7.45 1.10e+00 8.26e-01 4.59e+01 angle pdb=" N PRO A 275 " pdb=" CA PRO A 275 " pdb=" CB PRO A 275 " ideal model delta sigma weight residual 103.00 110.44 -7.44 1.10e+00 8.26e-01 4.58e+01 angle pdb=" C ASN B 612 " pdb=" N VAL B 613 " pdb=" CA VAL B 613 " ideal model delta sigma weight residual 123.16 117.82 5.34 1.06e+00 8.90e-01 2.54e+01 angle pdb=" C ASN A 612 " pdb=" N VAL A 613 " pdb=" CA VAL A 613 " ideal model delta sigma weight residual 123.16 117.85 5.31 1.06e+00 8.90e-01 2.51e+01 angle pdb=" N ILE B 714 " pdb=" CA ILE B 714 " pdb=" C ILE B 714 " ideal model delta sigma weight residual 109.34 101.30 8.04 2.08e+00 2.31e-01 1.49e+01 ... (remaining 13433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 5193 17.43 - 34.87: 407 34.87 - 52.30: 94 52.30 - 69.74: 28 69.74 - 87.17: 8 Dihedral angle restraints: 5730 sinusoidal: 2132 harmonic: 3598 Sorted by residual: dihedral pdb=" CA LEU A 703 " pdb=" C LEU A 703 " pdb=" N ASN A 704 " pdb=" CA ASN A 704 " ideal model delta harmonic sigma weight residual 180.00 156.95 23.05 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA LEU B 703 " pdb=" C LEU B 703 " pdb=" N ASN B 704 " pdb=" CA ASN B 704 " ideal model delta harmonic sigma weight residual 180.00 156.99 23.01 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA ASP B 316 " pdb=" C ASP B 316 " pdb=" N GLN B 317 " pdb=" CA GLN B 317 " ideal model delta harmonic sigma weight residual 180.00 -160.13 -19.87 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 5727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1176 0.049 - 0.098: 318 0.098 - 0.147: 44 0.147 - 0.195: 4 0.195 - 0.244: 6 Chirality restraints: 1548 Sorted by residual: chirality pdb=" CA PRO B 275 " pdb=" N PRO B 275 " pdb=" C PRO B 275 " pdb=" CB PRO B 275 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA PRO A 275 " pdb=" N PRO A 275 " pdb=" C PRO A 275 " pdb=" CB PRO A 275 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ILE B 714 " pdb=" N ILE B 714 " pdb=" C ILE B 714 " pdb=" CB ILE B 714 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 1545 not shown) Planarity restraints: 1666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 715 " 0.050 5.00e-02 4.00e+02 7.56e-02 9.15e+00 pdb=" N PRO A 716 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 716 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 716 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 715 " -0.050 5.00e-02 4.00e+02 7.56e-02 9.14e+00 pdb=" N PRO B 716 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO B 716 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 716 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 181 " 0.007 2.00e-02 2.50e+03 1.44e-02 4.16e+00 pdb=" CG TYR B 181 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR B 181 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR B 181 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR B 181 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 181 " -0.028 2.00e-02 2.50e+03 pdb=" CZ TYR B 181 " 0.020 2.00e-02 2.50e+03 pdb=" OH TYR B 181 " 0.004 2.00e-02 2.50e+03 ... (remaining 1663 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2523 2.79 - 3.32: 10181 3.32 - 3.84: 17986 3.84 - 4.37: 20781 4.37 - 4.90: 33304 Nonbonded interactions: 84775 Sorted by model distance: nonbonded pdb=" O ASN B 208 " pdb=" N TRP B 349 " model vdw 2.259 3.120 nonbonded pdb=" O ASN A 208 " pdb=" N TRP A 349 " model vdw 2.259 3.120 nonbonded pdb=" O ALA A 91 " pdb=" OG SER A 95 " model vdw 2.271 3.040 nonbonded pdb=" O ALA B 91 " pdb=" OG SER B 95 " model vdw 2.271 3.040 nonbonded pdb=" O ILE A 13 " pdb=" OG1 THR A 17 " model vdw 2.278 3.040 ... (remaining 84770 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: 0.02 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.050 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 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 : 0.005 0.066 9854 Z= 0.215 Angle : 0.755 8.207 13438 Z= 0.414 Chirality : 0.045 0.244 1548 Planarity : 0.006 0.076 1666 Dihedral : 14.349 87.173 3390 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.45 % Favored : 94.04 % Rotamer: Outliers : 4.55 % Allowed : 13.04 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.54 (0.21), residues: 1192 helix: -1.88 (0.15), residues: 832 sheet: -3.40 (0.87), residues: 24 loop : -3.03 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 331 TYR 0.028 0.002 TYR B 181 PHE 0.017 0.002 PHE B 669 TRP 0.022 0.002 TRP B 625 HIS 0.009 0.002 HIS B 608 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 9854) covalent geometry : angle 0.75461 (13438) hydrogen bonds : bond 0.11189 ( 655) hydrogen bonds : angle 6.57705 ( 1959) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 398 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 17 THR cc_start: 0.9303 (m) cc_final: 0.8673 (t) REVERT: A 21 PHE cc_start: 0.8884 (m-10) cc_final: 0.8658 (m-80) REVERT: A 86 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8432 (tp30) REVERT: A 89 ASP cc_start: 0.9066 (t70) cc_final: 0.8840 (t0) REVERT: A 94 ASP cc_start: 0.8651 (p0) cc_final: 0.8329 (p0) REVERT: A 102 TYR cc_start: 0.8961 (m-80) cc_final: 0.8743 (m-10) REVERT: A 115 LEU cc_start: 0.9365 (tt) cc_final: 0.9041 (tt) REVERT: A 190 GLN cc_start: 0.8650 (tt0) cc_final: 0.8141 (tm-30) REVERT: A 201 GLN cc_start: 0.8607 (mt0) cc_final: 0.8214 (mp10) REVERT: A 208 ASN cc_start: 0.8504 (m-40) cc_final: 0.8221 (m-40) REVERT: A 226 LEU cc_start: 0.9431 (mt) cc_final: 0.9091 (mt) REVERT: A 247 ASP cc_start: 0.8101 (t70) cc_final: 0.7779 (t0) REVERT: A 260 ASP cc_start: 0.8733 (m-30) cc_final: 0.8271 (t0) REVERT: A 361 TYR cc_start: 0.9014 (t80) cc_final: 0.8305 (t80) REVERT: A 363 PRO cc_start: 0.9530 (Cg_exo) cc_final: 0.9098 (Cg_endo) REVERT: A 364 ASN cc_start: 0.9112 (t0) cc_final: 0.8857 (t0) REVERT: A 376 ARG cc_start: 0.8461 (ttm110) cc_final: 0.8187 (mtm-85) REVERT: A 438 PHE cc_start: 0.8978 (m-10) cc_final: 0.8628 (m-10) REVERT: A 441 PHE cc_start: 0.8731 (m-80) cc_final: 0.8443 (m-80) REVERT: A 452 PHE cc_start: 0.9273 (t80) cc_final: 0.8725 (t80) REVERT: A 460 PHE cc_start: 0.8743 (t80) cc_final: 0.8531 (t80) REVERT: A 524 ASP cc_start: 0.9250 (t0) cc_final: 0.8998 (t70) REVERT: A 539 LEU cc_start: 0.9165 (tt) cc_final: 0.8962 (tp) REVERT: A 616 GLN cc_start: 0.8801 (mm110) cc_final: 0.8486 (mm110) REVERT: A 633 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8840 (tp) REVERT: A 644 MET cc_start: 0.8496 (mtp) cc_final: 0.7983 (tmm) REVERT: A 688 GLU cc_start: 0.9270 (mm-30) cc_final: 0.9038 (mm-30) REVERT: B 86 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8472 (tp30) REVERT: B 94 ASP cc_start: 0.8693 (p0) cc_final: 0.8375 (p0) REVERT: B 102 TYR cc_start: 0.9075 (m-80) cc_final: 0.8869 (m-10) REVERT: B 115 LEU cc_start: 0.9333 (tt) cc_final: 0.9013 (tt) REVERT: B 201 GLN cc_start: 0.8600 (mt0) cc_final: 0.8172 (mp10) REVERT: B 208 ASN cc_start: 0.8672 (m-40) cc_final: 0.8387 (m-40) REVERT: B 222 GLU cc_start: 0.8542 (tm-30) cc_final: 0.7946 (tm-30) REVERT: B 226 LEU cc_start: 0.9350 (mt) cc_final: 0.8933 (mt) REVERT: B 260 ASP cc_start: 0.8704 (m-30) cc_final: 0.8253 (t70) REVERT: B 361 TYR cc_start: 0.9009 (t80) cc_final: 0.8456 (t80) REVERT: B 364 ASN cc_start: 0.9156 (t0) cc_final: 0.8834 (t0) REVERT: B 376 ARG cc_start: 0.8341 (ttm110) cc_final: 0.8116 (mtm-85) REVERT: B 438 PHE cc_start: 0.9083 (m-10) cc_final: 0.8711 (m-10) REVERT: B 441 PHE cc_start: 0.8867 (m-80) cc_final: 0.8597 (m-80) REVERT: B 452 PHE cc_start: 0.9305 (t80) cc_final: 0.8729 (t80) REVERT: B 460 PHE cc_start: 0.8580 (t80) cc_final: 0.8366 (t80) REVERT: B 524 ASP cc_start: 0.9291 (t0) cc_final: 0.9015 (t70) REVERT: B 539 LEU cc_start: 0.9258 (tt) cc_final: 0.9030 (tp) REVERT: B 616 GLN cc_start: 0.8844 (mm110) cc_final: 0.8578 (mm110) REVERT: B 633 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8827 (tp) REVERT: B 644 MET cc_start: 0.8440 (mtp) cc_final: 0.7855 (tmm) REVERT: B 688 GLU cc_start: 0.9262 (mm-30) cc_final: 0.8978 (mm-30) outliers start: 44 outliers final: 13 residues processed: 418 average time/residue: 0.0805 time to fit residues: 49.1960 Evaluate side-chains 305 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 288 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 634 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.121782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.104142 restraints weight = 18698.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.107400 restraints weight = 8242.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.109550 restraints weight = 4825.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.110787 restraints weight = 3365.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.111722 restraints weight = 2700.467| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9854 Z= 0.166 Angle : 0.734 8.381 13438 Z= 0.370 Chirality : 0.044 0.169 1548 Planarity : 0.006 0.065 1666 Dihedral : 7.477 56.638 1342 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 6.00 % Allowed : 19.46 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.23), residues: 1192 helix: -0.70 (0.16), residues: 856 sheet: -3.68 (0.92), residues: 24 loop : -2.93 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 468 TYR 0.020 0.002 TYR B 181 PHE 0.043 0.002 PHE B 21 TRP 0.020 0.002 TRP A 625 HIS 0.004 0.001 HIS B 608 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 9854) covalent geometry : angle 0.73397 (13438) hydrogen bonds : bond 0.04269 ( 655) hydrogen bonds : angle 5.01296 ( 1959) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 339 time to evaluate : 0.347 Fit side-chains REVERT: A 17 THR cc_start: 0.9237 (m) cc_final: 0.8559 (t) REVERT: A 30 LEU cc_start: 0.8833 (mt) cc_final: 0.8529 (pp) REVERT: A 36 ARG cc_start: 0.8985 (mtp180) cc_final: 0.8619 (ttm-80) REVERT: A 115 LEU cc_start: 0.9385 (tt) cc_final: 0.9110 (tt) REVERT: A 176 MET cc_start: 0.8385 (tpp) cc_final: 0.7967 (tpp) REVERT: A 201 GLN cc_start: 0.8630 (mt0) cc_final: 0.8207 (mp10) REVERT: A 208 ASN cc_start: 0.8186 (m-40) cc_final: 0.7938 (m-40) REVERT: A 226 LEU cc_start: 0.9264 (mt) cc_final: 0.8875 (mt) REVERT: A 247 ASP cc_start: 0.7523 (t70) cc_final: 0.7073 (t0) REVERT: A 257 ASN cc_start: 0.9037 (p0) cc_final: 0.8752 (m-40) REVERT: A 360 ILE cc_start: 0.9097 (pt) cc_final: 0.8875 (pt) REVERT: A 361 TYR cc_start: 0.8560 (t80) cc_final: 0.7755 (t80) REVERT: A 363 PRO cc_start: 0.9350 (Cg_exo) cc_final: 0.8789 (Cg_endo) REVERT: A 376 ARG cc_start: 0.8337 (ttm110) cc_final: 0.8118 (mtm-85) REVERT: A 438 PHE cc_start: 0.8787 (m-10) cc_final: 0.8470 (m-10) REVERT: A 441 PHE cc_start: 0.7876 (m-80) cc_final: 0.7577 (m-80) REVERT: A 465 SER cc_start: 0.9279 (t) cc_final: 0.8990 (m) REVERT: A 479 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7621 (mp) REVERT: A 524 ASP cc_start: 0.9027 (t0) cc_final: 0.8785 (t70) REVERT: A 688 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8154 (mm-30) REVERT: B 30 LEU cc_start: 0.8836 (mt) cc_final: 0.8546 (pp) REVERT: B 36 ARG cc_start: 0.8596 (mmm160) cc_final: 0.8325 (mmm160) REVERT: B 72 PHE cc_start: 0.6616 (t80) cc_final: 0.6412 (t80) REVERT: B 94 ASP cc_start: 0.8004 (p0) cc_final: 0.7605 (p0) REVERT: B 115 LEU cc_start: 0.9377 (tt) cc_final: 0.8927 (tt) REVERT: B 208 ASN cc_start: 0.8268 (m-40) cc_final: 0.7992 (m-40) REVERT: B 226 LEU cc_start: 0.9209 (mt) cc_final: 0.8878 (mt) REVERT: B 247 ASP cc_start: 0.7507 (t70) cc_final: 0.7192 (t0) REVERT: B 257 ASN cc_start: 0.8446 (m-40) cc_final: 0.8090 (p0) REVERT: B 260 ASP cc_start: 0.8457 (m-30) cc_final: 0.8116 (t0) REVERT: B 344 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8179 (ttm110) REVERT: B 360 ILE cc_start: 0.9081 (pt) cc_final: 0.8820 (pt) REVERT: B 361 TYR cc_start: 0.8617 (t80) cc_final: 0.8373 (t80) REVERT: B 376 ARG cc_start: 0.8257 (ttm110) cc_final: 0.8046 (mtm-85) REVERT: B 430 LEU cc_start: 0.8135 (tp) cc_final: 0.7849 (tt) REVERT: B 438 PHE cc_start: 0.8946 (m-10) cc_final: 0.8616 (m-10) REVERT: B 441 PHE cc_start: 0.7981 (m-80) cc_final: 0.7661 (m-80) REVERT: B 479 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7456 (mp) REVERT: B 522 MET cc_start: 0.8619 (mmm) cc_final: 0.7842 (mmp) REVERT: B 565 ILE cc_start: 0.9176 (tp) cc_final: 0.8893 (tp) REVERT: B 633 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8640 (tp) REVERT: B 644 MET cc_start: 0.7337 (mtp) cc_final: 0.7136 (tmm) REVERT: B 686 LEU cc_start: 0.9487 (mt) cc_final: 0.9239 (mt) outliers start: 58 outliers final: 26 residues processed: 376 average time/residue: 0.0723 time to fit residues: 40.8743 Evaluate side-chains 329 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 299 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 714 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 31 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 GLN ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 HIS B 575 GLN ** B 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.125524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.107851 restraints weight = 18306.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.111220 restraints weight = 8221.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.113403 restraints weight = 4860.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.114672 restraints weight = 3415.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.115661 restraints weight = 2738.587| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9854 Z= 0.166 Angle : 0.706 9.224 13438 Z= 0.359 Chirality : 0.044 0.168 1548 Planarity : 0.005 0.059 1666 Dihedral : 6.387 52.010 1332 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 6.52 % Allowed : 21.95 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.24), residues: 1192 helix: -0.19 (0.17), residues: 838 sheet: -3.96 (0.88), residues: 24 loop : -2.52 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 344 TYR 0.019 0.002 TYR A 102 PHE 0.018 0.002 PHE B 598 TRP 0.020 0.002 TRP A 625 HIS 0.004 0.001 HIS B 294 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 9854) covalent geometry : angle 0.70609 (13438) hydrogen bonds : bond 0.04060 ( 655) hydrogen bonds : angle 4.83258 ( 1959) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 335 time to evaluate : 0.361 Fit side-chains REVERT: A 21 PHE cc_start: 0.8930 (m-80) cc_final: 0.8492 (m-80) REVERT: A 36 ARG cc_start: 0.8942 (mtp180) cc_final: 0.8707 (tpp80) REVERT: A 76 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.8044 (tpp) REVERT: A 94 ASP cc_start: 0.7928 (p0) cc_final: 0.7651 (p0) REVERT: A 102 TYR cc_start: 0.8456 (m-10) cc_final: 0.8241 (m-10) REVERT: A 115 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9042 (tt) REVERT: A 226 LEU cc_start: 0.9226 (mt) cc_final: 0.8952 (mt) REVERT: A 260 ASP cc_start: 0.8313 (t70) cc_final: 0.7831 (t70) REVERT: A 361 TYR cc_start: 0.8613 (t80) cc_final: 0.7914 (t80) REVERT: A 363 PRO cc_start: 0.9306 (Cg_exo) cc_final: 0.8975 (Cg_endo) REVERT: A 376 ARG cc_start: 0.8272 (ttm110) cc_final: 0.8019 (mtm-85) REVERT: A 438 PHE cc_start: 0.8817 (m-10) cc_final: 0.8464 (m-10) REVERT: A 441 PHE cc_start: 0.7724 (m-80) cc_final: 0.7476 (m-80) REVERT: A 460 PHE cc_start: 0.8330 (t80) cc_final: 0.8055 (t80) REVERT: A 465 SER cc_start: 0.9278 (t) cc_final: 0.9012 (m) REVERT: A 479 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7618 (mp) REVERT: A 522 MET cc_start: 0.8661 (mmm) cc_final: 0.7502 (mmp) REVERT: A 524 ASP cc_start: 0.8960 (t0) cc_final: 0.8707 (t70) REVERT: A 526 TRP cc_start: 0.8405 (m-10) cc_final: 0.8188 (m-10) REVERT: A 640 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8434 (mm-40) REVERT: A 688 GLU cc_start: 0.8456 (mm-30) cc_final: 0.7809 (mm-30) REVERT: B 21 PHE cc_start: 0.8771 (m-80) cc_final: 0.8375 (m-80) REVERT: B 30 LEU cc_start: 0.8781 (mt) cc_final: 0.8538 (pp) REVERT: B 94 ASP cc_start: 0.7784 (p0) cc_final: 0.7571 (p0) REVERT: B 102 TYR cc_start: 0.8463 (m-10) cc_final: 0.8219 (m-10) REVERT: B 115 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9063 (tt) REVERT: B 176 MET cc_start: 0.8085 (tpp) cc_final: 0.7809 (tpp) REVERT: B 197 ARG cc_start: 0.7816 (ttm110) cc_final: 0.7318 (mtm-85) REVERT: B 226 LEU cc_start: 0.9190 (mt) cc_final: 0.8896 (mt) REVERT: B 247 ASP cc_start: 0.7149 (t70) cc_final: 0.6762 (t0) REVERT: B 344 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8035 (ttm110) REVERT: B 361 TYR cc_start: 0.8696 (t80) cc_final: 0.7961 (t80) REVERT: B 363 PRO cc_start: 0.9337 (Cg_exo) cc_final: 0.8909 (Cg_endo) REVERT: B 376 ARG cc_start: 0.8219 (ttm110) cc_final: 0.7982 (mtm-85) REVERT: B 430 LEU cc_start: 0.8008 (tp) cc_final: 0.7698 (tt) REVERT: B 438 PHE cc_start: 0.8943 (m-10) cc_final: 0.8614 (m-10) REVERT: B 441 PHE cc_start: 0.7805 (m-80) cc_final: 0.7479 (m-80) REVERT: B 447 MET cc_start: 0.9067 (tpt) cc_final: 0.8761 (tpp) REVERT: B 460 PHE cc_start: 0.8356 (t80) cc_final: 0.8135 (t80) REVERT: B 479 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7537 (mp) REVERT: B 522 MET cc_start: 0.8615 (mmm) cc_final: 0.7961 (mmp) REVERT: B 616 GLN cc_start: 0.7924 (mm-40) cc_final: 0.7500 (mm-40) REVERT: B 686 LEU cc_start: 0.9500 (mt) cc_final: 0.9294 (mt) outliers start: 63 outliers final: 33 residues processed: 365 average time/residue: 0.0713 time to fit residues: 39.7074 Evaluate side-chains 337 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 298 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 613 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 96 optimal weight: 0.3980 chunk 50 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 116 optimal weight: 0.0050 chunk 70 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 ASN ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.128695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.111093 restraints weight = 18526.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.114454 restraints weight = 8360.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.116457 restraints weight = 4919.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.117901 restraints weight = 3513.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.118722 restraints weight = 2766.750| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9854 Z= 0.145 Angle : 0.699 10.223 13438 Z= 0.348 Chirality : 0.043 0.188 1548 Planarity : 0.005 0.057 1666 Dihedral : 6.189 50.630 1328 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 5.59 % Allowed : 25.16 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.24), residues: 1192 helix: -0.02 (0.17), residues: 848 sheet: -4.07 (0.89), residues: 24 loop : -2.52 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 331 TYR 0.027 0.002 TYR B 577 PHE 0.023 0.002 PHE A 396 TRP 0.018 0.001 TRP A 625 HIS 0.004 0.001 HIS A 608 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9854) covalent geometry : angle 0.69891 (13438) hydrogen bonds : bond 0.03769 ( 655) hydrogen bonds : angle 4.70106 ( 1959) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 331 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 21 PHE cc_start: 0.8756 (m-80) cc_final: 0.8109 (m-80) REVERT: A 30 LEU cc_start: 0.8686 (mt) cc_final: 0.8454 (pp) REVERT: A 36 ARG cc_start: 0.8956 (mtp180) cc_final: 0.8366 (tpp80) REVERT: A 75 TRP cc_start: 0.7599 (t60) cc_final: 0.7210 (t60) REVERT: A 76 MET cc_start: 0.8233 (tpp) cc_final: 0.7463 (tpp) REVERT: A 115 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.8957 (tt) REVERT: A 167 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.7667 (t80) REVERT: A 176 MET cc_start: 0.8081 (tpp) cc_final: 0.7625 (tpp) REVERT: A 226 LEU cc_start: 0.9195 (mt) cc_final: 0.8922 (mt) REVERT: A 247 ASP cc_start: 0.7484 (t70) cc_final: 0.6995 (t0) REVERT: A 260 ASP cc_start: 0.8286 (t70) cc_final: 0.8008 (t70) REVERT: A 337 CYS cc_start: 0.8625 (t) cc_final: 0.8419 (t) REVERT: A 361 TYR cc_start: 0.8540 (t80) cc_final: 0.7868 (t80) REVERT: A 363 PRO cc_start: 0.9215 (Cg_exo) cc_final: 0.8894 (Cg_endo) REVERT: A 376 ARG cc_start: 0.8257 (ttm110) cc_final: 0.8021 (mtm-85) REVERT: A 438 PHE cc_start: 0.8804 (m-10) cc_final: 0.8455 (m-10) REVERT: A 441 PHE cc_start: 0.7678 (m-80) cc_final: 0.7407 (m-80) REVERT: A 452 PHE cc_start: 0.8946 (t80) cc_final: 0.8602 (t80) REVERT: A 465 SER cc_start: 0.9296 (t) cc_final: 0.8993 (m) REVERT: A 479 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7567 (mp) REVERT: A 524 ASP cc_start: 0.9004 (t0) cc_final: 0.8605 (t70) REVERT: A 644 MET cc_start: 0.7374 (mmm) cc_final: 0.6175 (tmm) REVERT: A 688 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7726 (mm-30) REVERT: A 710 GLN cc_start: 0.8399 (pt0) cc_final: 0.8131 (tm-30) REVERT: B 21 PHE cc_start: 0.8739 (m-80) cc_final: 0.8044 (m-80) REVERT: B 82 MET cc_start: 0.8052 (tpt) cc_final: 0.7792 (ttt) REVERT: B 94 ASP cc_start: 0.7902 (p0) cc_final: 0.7683 (p0) REVERT: B 102 TYR cc_start: 0.8491 (m-10) cc_final: 0.8242 (m-10) REVERT: B 115 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.8856 (tt) REVERT: B 226 LEU cc_start: 0.9184 (mt) cc_final: 0.8904 (mt) REVERT: B 336 VAL cc_start: 0.8751 (OUTLIER) cc_final: 0.8549 (p) REVERT: B 344 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7996 (ttm110) REVERT: B 361 TYR cc_start: 0.8569 (t80) cc_final: 0.7898 (t80) REVERT: B 363 PRO cc_start: 0.9303 (Cg_exo) cc_final: 0.8849 (Cg_endo) REVERT: B 376 ARG cc_start: 0.8203 (ttm110) cc_final: 0.7952 (mtm-85) REVERT: B 430 LEU cc_start: 0.8112 (tp) cc_final: 0.7902 (tt) REVERT: B 438 PHE cc_start: 0.8976 (m-10) cc_final: 0.8622 (m-10) REVERT: B 441 PHE cc_start: 0.7733 (m-80) cc_final: 0.7480 (m-80) REVERT: B 447 MET cc_start: 0.9053 (tpt) cc_final: 0.8744 (tpp) REVERT: B 479 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7519 (mp) REVERT: B 522 MET cc_start: 0.8559 (mmm) cc_final: 0.7523 (mmp) REVERT: B 526 TRP cc_start: 0.8496 (m-10) cc_final: 0.8086 (m-10) REVERT: B 577 TYR cc_start: 0.7456 (m-80) cc_final: 0.7234 (m-80) REVERT: B 616 GLN cc_start: 0.7694 (mm-40) cc_final: 0.7374 (mm-40) REVERT: B 686 LEU cc_start: 0.9484 (mt) cc_final: 0.9251 (mt) outliers start: 54 outliers final: 38 residues processed: 355 average time/residue: 0.0753 time to fit residues: 39.6566 Evaluate side-chains 330 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 285 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 575 GLN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 678 GLU Chi-restraints excluded: chain B residue 691 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 65 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 121 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.128310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.111071 restraints weight = 18471.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.114360 restraints weight = 8340.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.116510 restraints weight = 4923.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.117768 restraints weight = 3443.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.118687 restraints weight = 2744.347| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9854 Z= 0.161 Angle : 0.710 10.461 13438 Z= 0.354 Chirality : 0.043 0.180 1548 Planarity : 0.005 0.060 1666 Dihedral : 6.238 57.445 1328 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 6.21 % Allowed : 25.36 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.24), residues: 1192 helix: 0.20 (0.18), residues: 842 sheet: -4.02 (0.91), residues: 24 loop : -2.48 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 468 TYR 0.028 0.002 TYR A 102 PHE 0.015 0.002 PHE A 669 TRP 0.022 0.001 TRP B 75 HIS 0.005 0.001 HIS B 608 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 9854) covalent geometry : angle 0.71025 (13438) hydrogen bonds : bond 0.03750 ( 655) hydrogen bonds : angle 4.64783 ( 1959) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 301 time to evaluate : 0.237 Fit side-chains REVERT: A 21 PHE cc_start: 0.8707 (m-80) cc_final: 0.8016 (m-80) REVERT: A 30 LEU cc_start: 0.8707 (mt) cc_final: 0.8488 (pp) REVERT: A 75 TRP cc_start: 0.7707 (t60) cc_final: 0.7314 (t60) REVERT: A 115 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9070 (tt) REVERT: A 176 MET cc_start: 0.8165 (tpp) cc_final: 0.7908 (tpp) REVERT: A 226 LEU cc_start: 0.9197 (mt) cc_final: 0.8923 (mt) REVERT: A 247 ASP cc_start: 0.7516 (t70) cc_final: 0.7023 (t0) REVERT: A 260 ASP cc_start: 0.8374 (t70) cc_final: 0.8095 (t70) REVERT: A 361 TYR cc_start: 0.8608 (t80) cc_final: 0.7970 (t80) REVERT: A 363 PRO cc_start: 0.9218 (Cg_exo) cc_final: 0.8838 (Cg_endo) REVERT: A 376 ARG cc_start: 0.8276 (ttm110) cc_final: 0.8007 (mtm-85) REVERT: A 438 PHE cc_start: 0.8781 (m-10) cc_final: 0.8385 (m-10) REVERT: A 441 PHE cc_start: 0.7656 (m-80) cc_final: 0.7382 (m-80) REVERT: A 452 PHE cc_start: 0.8940 (t80) cc_final: 0.8138 (t80) REVERT: A 460 PHE cc_start: 0.8449 (t80) cc_final: 0.8217 (t80) REVERT: A 465 SER cc_start: 0.9312 (t) cc_final: 0.9013 (m) REVERT: A 478 PHE cc_start: 0.9034 (t80) cc_final: 0.8794 (t80) REVERT: A 479 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7601 (mp) REVERT: A 510 ILE cc_start: 0.7340 (OUTLIER) cc_final: 0.7080 (mt) REVERT: A 522 MET cc_start: 0.8851 (mmp) cc_final: 0.8456 (mmp) REVERT: A 524 ASP cc_start: 0.9053 (t0) cc_final: 0.8622 (t70) REVERT: A 584 TYR cc_start: 0.8626 (m-10) cc_final: 0.8042 (m-10) REVERT: A 644 MET cc_start: 0.7526 (mmm) cc_final: 0.6259 (tmm) REVERT: A 688 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7643 (mm-30) REVERT: B 21 PHE cc_start: 0.8691 (m-80) cc_final: 0.7983 (m-80) REVERT: B 102 TYR cc_start: 0.8511 (m-10) cc_final: 0.8250 (m-10) REVERT: B 115 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9077 (tt) REVERT: B 226 LEU cc_start: 0.9194 (mt) cc_final: 0.8886 (mt) REVERT: B 303 SER cc_start: 0.9121 (t) cc_final: 0.8907 (p) REVERT: B 337 CYS cc_start: 0.8696 (t) cc_final: 0.8490 (t) REVERT: B 344 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7995 (ttm110) REVERT: B 361 TYR cc_start: 0.8597 (t80) cc_final: 0.7973 (t80) REVERT: B 363 PRO cc_start: 0.9268 (Cg_exo) cc_final: 0.8876 (Cg_endo) REVERT: B 376 ARG cc_start: 0.8221 (ttm110) cc_final: 0.7989 (mtm-85) REVERT: B 430 LEU cc_start: 0.8219 (tp) cc_final: 0.7989 (tt) REVERT: B 438 PHE cc_start: 0.8984 (m-10) cc_final: 0.8644 (m-10) REVERT: B 441 PHE cc_start: 0.7690 (m-80) cc_final: 0.7434 (m-80) REVERT: B 447 MET cc_start: 0.8977 (tpt) cc_final: 0.8637 (tpp) REVERT: B 460 PHE cc_start: 0.8424 (t80) cc_final: 0.8185 (t80) REVERT: B 465 SER cc_start: 0.9365 (t) cc_final: 0.9005 (m) REVERT: B 479 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7568 (mp) REVERT: B 522 MET cc_start: 0.8550 (mmm) cc_final: 0.8031 (mmp) REVERT: B 526 TRP cc_start: 0.8442 (m-10) cc_final: 0.8178 (m-10) REVERT: B 577 TYR cc_start: 0.7705 (m-80) cc_final: 0.7381 (m-80) outliers start: 60 outliers final: 40 residues processed: 331 average time/residue: 0.0688 time to fit residues: 35.0446 Evaluate side-chains 331 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 285 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 673 CYS Chi-restraints excluded: chain B residue 678 GLU Chi-restraints excluded: chain B residue 691 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 115 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 119 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 108 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 GLN B 14 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.129491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.112479 restraints weight = 18489.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.115826 restraints weight = 8320.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.117986 restraints weight = 4865.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.119265 restraints weight = 3386.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.119914 restraints weight = 2681.568| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9854 Z= 0.151 Angle : 0.689 10.866 13438 Z= 0.344 Chirality : 0.043 0.166 1548 Planarity : 0.005 0.057 1666 Dihedral : 5.867 48.635 1326 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 5.28 % Allowed : 27.33 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.25), residues: 1192 helix: 0.38 (0.18), residues: 828 sheet: -3.87 (0.92), residues: 24 loop : -2.16 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 683 TYR 0.032 0.002 TYR A 102 PHE 0.025 0.001 PHE B 396 TRP 0.018 0.001 TRP A 625 HIS 0.004 0.001 HIS A 608 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 9854) covalent geometry : angle 0.68853 (13438) hydrogen bonds : bond 0.03703 ( 655) hydrogen bonds : angle 4.60717 ( 1959) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 297 time to evaluate : 0.347 Fit side-chains REVERT: A 30 LEU cc_start: 0.8765 (mt) cc_final: 0.8541 (pp) REVERT: A 115 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9089 (tt) REVERT: A 176 MET cc_start: 0.8305 (tpp) cc_final: 0.7979 (tpp) REVERT: A 226 LEU cc_start: 0.9185 (mt) cc_final: 0.8918 (mt) REVERT: A 247 ASP cc_start: 0.7440 (t70) cc_final: 0.6932 (t0) REVERT: A 296 ILE cc_start: 0.8306 (mm) cc_final: 0.7884 (tp) REVERT: A 361 TYR cc_start: 0.8595 (t80) cc_final: 0.7958 (t80) REVERT: A 363 PRO cc_start: 0.9232 (Cg_exo) cc_final: 0.8876 (Cg_endo) REVERT: A 376 ARG cc_start: 0.8186 (ttm110) cc_final: 0.7977 (mtm-85) REVERT: A 441 PHE cc_start: 0.7675 (m-80) cc_final: 0.7397 (m-80) REVERT: A 452 PHE cc_start: 0.9007 (t80) cc_final: 0.8289 (t80) REVERT: A 465 SER cc_start: 0.9298 (t) cc_final: 0.9009 (m) REVERT: A 479 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7651 (mp) REVERT: A 522 MET cc_start: 0.8862 (mmp) cc_final: 0.8369 (mmp) REVERT: A 577 TYR cc_start: 0.7671 (m-10) cc_final: 0.7397 (m-10) REVERT: A 688 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7713 (mm-30) REVERT: B 94 ASP cc_start: 0.7850 (p0) cc_final: 0.7477 (p0) REVERT: B 102 TYR cc_start: 0.8652 (m-10) cc_final: 0.8396 (m-10) REVERT: B 115 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9004 (tt) REVERT: B 121 VAL cc_start: 0.5207 (OUTLIER) cc_final: 0.4884 (p) REVERT: B 176 MET cc_start: 0.7969 (tpp) cc_final: 0.7492 (tpp) REVERT: B 226 LEU cc_start: 0.9197 (mt) cc_final: 0.8896 (mt) REVERT: B 303 SER cc_start: 0.9118 (t) cc_final: 0.8900 (p) REVERT: B 344 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.7940 (ttm110) REVERT: B 361 TYR cc_start: 0.8632 (t80) cc_final: 0.7996 (t80) REVERT: B 363 PRO cc_start: 0.9317 (Cg_exo) cc_final: 0.9016 (Cg_endo) REVERT: B 376 ARG cc_start: 0.8285 (ttm110) cc_final: 0.8004 (mtm-85) REVERT: B 430 LEU cc_start: 0.8161 (tp) cc_final: 0.7941 (tt) REVERT: B 438 PHE cc_start: 0.8990 (m-10) cc_final: 0.8621 (m-10) REVERT: B 441 PHE cc_start: 0.7694 (m-80) cc_final: 0.7444 (m-80) REVERT: B 447 MET cc_start: 0.8986 (tpt) cc_final: 0.8669 (tpp) REVERT: B 460 PHE cc_start: 0.8358 (t80) cc_final: 0.8119 (t80) REVERT: B 465 SER cc_start: 0.9342 (t) cc_final: 0.9003 (m) REVERT: B 479 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7586 (mp) REVERT: B 522 MET cc_start: 0.8591 (mmm) cc_final: 0.8009 (mmp) REVERT: B 526 TRP cc_start: 0.8391 (m-10) cc_final: 0.8166 (m-10) REVERT: B 560 MET cc_start: 0.5175 (ttm) cc_final: 0.4972 (ttm) REVERT: B 686 LEU cc_start: 0.9485 (mt) cc_final: 0.9272 (mt) outliers start: 51 outliers final: 37 residues processed: 318 average time/residue: 0.0732 time to fit residues: 35.4967 Evaluate side-chains 319 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 276 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 673 CYS Chi-restraints excluded: chain B residue 691 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 78 optimal weight: 0.7980 chunk 10 optimal weight: 0.0570 chunk 103 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 109 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.130961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.114199 restraints weight = 18534.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.117596 restraints weight = 8269.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.119778 restraints weight = 4793.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.121021 restraints weight = 3307.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.121806 restraints weight = 2617.587| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9854 Z= 0.146 Angle : 0.714 11.124 13438 Z= 0.351 Chirality : 0.043 0.186 1548 Planarity : 0.005 0.054 1666 Dihedral : 5.581 44.181 1322 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 5.38 % Allowed : 28.16 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.25), residues: 1192 helix: 0.46 (0.18), residues: 828 sheet: -3.91 (0.94), residues: 24 loop : -2.28 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 683 TYR 0.045 0.002 TYR B 577 PHE 0.030 0.001 PHE B 169 TRP 0.023 0.002 TRP A 75 HIS 0.004 0.001 HIS B 608 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9854) covalent geometry : angle 0.71371 (13438) hydrogen bonds : bond 0.03660 ( 655) hydrogen bonds : angle 4.59398 ( 1959) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 294 time to evaluate : 0.362 Fit side-chains REVERT: A 76 MET cc_start: 0.7984 (tpp) cc_final: 0.7580 (mmm) REVERT: A 115 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9090 (tt) REVERT: A 176 MET cc_start: 0.8377 (tpp) cc_final: 0.7962 (tpp) REVERT: A 226 LEU cc_start: 0.9198 (mt) cc_final: 0.8851 (mt) REVERT: A 247 ASP cc_start: 0.7410 (t70) cc_final: 0.6895 (t0) REVERT: A 361 TYR cc_start: 0.8552 (t80) cc_final: 0.7946 (t80) REVERT: A 363 PRO cc_start: 0.9225 (Cg_exo) cc_final: 0.8869 (Cg_endo) REVERT: A 376 ARG cc_start: 0.8237 (ttm110) cc_final: 0.7981 (mtm-85) REVERT: A 441 PHE cc_start: 0.7625 (m-80) cc_final: 0.7365 (m-80) REVERT: A 465 SER cc_start: 0.9293 (t) cc_final: 0.8984 (m) REVERT: A 479 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7641 (mp) REVERT: A 522 MET cc_start: 0.8884 (mmp) cc_final: 0.8382 (mmp) REVERT: A 532 GLU cc_start: 0.6314 (tp30) cc_final: 0.5964 (tp30) REVERT: A 577 TYR cc_start: 0.7599 (m-10) cc_final: 0.7344 (m-10) REVERT: A 584 TYR cc_start: 0.8542 (m-10) cc_final: 0.8305 (m-10) REVERT: A 644 MET cc_start: 0.7625 (mmm) cc_final: 0.6179 (tmm) REVERT: A 688 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7739 (mm-30) REVERT: B 42 TRP cc_start: 0.8294 (m100) cc_final: 0.7636 (m100) REVERT: B 82 MET cc_start: 0.8437 (tpp) cc_final: 0.8066 (ttt) REVERT: B 86 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8270 (mt-10) REVERT: B 121 VAL cc_start: 0.5121 (OUTLIER) cc_final: 0.4787 (p) REVERT: B 226 LEU cc_start: 0.9175 (mt) cc_final: 0.8866 (mt) REVERT: B 303 SER cc_start: 0.9107 (t) cc_final: 0.8891 (p) REVERT: B 344 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.7944 (ttm110) REVERT: B 361 TYR cc_start: 0.8619 (t80) cc_final: 0.7991 (t80) REVERT: B 363 PRO cc_start: 0.9296 (Cg_exo) cc_final: 0.8981 (Cg_endo) REVERT: B 376 ARG cc_start: 0.8249 (ttm110) cc_final: 0.8017 (mtm-85) REVERT: B 430 LEU cc_start: 0.8233 (tp) cc_final: 0.8012 (tt) REVERT: B 438 PHE cc_start: 0.8942 (m-10) cc_final: 0.8588 (m-10) REVERT: B 441 PHE cc_start: 0.7661 (m-80) cc_final: 0.7401 (m-80) REVERT: B 447 MET cc_start: 0.8965 (tpt) cc_final: 0.8659 (tpp) REVERT: B 460 PHE cc_start: 0.8317 (t80) cc_final: 0.8096 (t80) REVERT: B 465 SER cc_start: 0.9322 (t) cc_final: 0.9005 (m) REVERT: B 479 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7622 (mp) REVERT: B 577 TYR cc_start: 0.7177 (m-80) cc_final: 0.6657 (m-80) REVERT: B 686 LEU cc_start: 0.9500 (mt) cc_final: 0.9296 (mt) outliers start: 52 outliers final: 40 residues processed: 316 average time/residue: 0.0722 time to fit residues: 34.6992 Evaluate side-chains 327 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 282 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 575 GLN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 673 CYS Chi-restraints excluded: chain B residue 678 GLU Chi-restraints excluded: chain B residue 691 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 26 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN A 575 GLN ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN B 575 GLN ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.131379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.114565 restraints weight = 18484.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.117993 restraints weight = 8283.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.120193 restraints weight = 4813.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.121613 restraints weight = 3312.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.122345 restraints weight = 2565.206| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9854 Z= 0.158 Angle : 0.717 10.999 13438 Z= 0.354 Chirality : 0.043 0.157 1548 Planarity : 0.005 0.054 1666 Dihedral : 5.688 55.955 1322 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 5.28 % Allowed : 28.99 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.25), residues: 1192 helix: 0.46 (0.18), residues: 826 sheet: -3.86 (0.97), residues: 24 loop : -2.32 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 631 TYR 0.046 0.002 TYR B 577 PHE 0.032 0.002 PHE B 396 TRP 0.052 0.002 TRP B 625 HIS 0.004 0.001 HIS A 608 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 9854) covalent geometry : angle 0.71684 (13438) hydrogen bonds : bond 0.03692 ( 655) hydrogen bonds : angle 4.57788 ( 1959) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 294 time to evaluate : 0.376 Fit side-chains REVERT: A 42 TRP cc_start: 0.8291 (m100) cc_final: 0.7751 (m100) REVERT: A 76 MET cc_start: 0.8004 (tpp) cc_final: 0.7581 (mmm) REVERT: A 115 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9163 (tt) REVERT: A 176 MET cc_start: 0.8481 (tpp) cc_final: 0.8050 (tpp) REVERT: A 226 LEU cc_start: 0.9213 (mt) cc_final: 0.8849 (mt) REVERT: A 247 ASP cc_start: 0.7406 (t70) cc_final: 0.6895 (t0) REVERT: A 260 ASP cc_start: 0.8309 (t70) cc_final: 0.8022 (t70) REVERT: A 296 ILE cc_start: 0.8244 (mm) cc_final: 0.7797 (tp) REVERT: A 361 TYR cc_start: 0.8600 (t80) cc_final: 0.7955 (t80) REVERT: A 363 PRO cc_start: 0.9237 (Cg_exo) cc_final: 0.8898 (Cg_endo) REVERT: A 376 ARG cc_start: 0.8241 (ttm110) cc_final: 0.8028 (mtm-85) REVERT: A 441 PHE cc_start: 0.7646 (m-80) cc_final: 0.7405 (m-80) REVERT: A 452 PHE cc_start: 0.8659 (t80) cc_final: 0.8190 (t80) REVERT: A 458 VAL cc_start: 0.8859 (OUTLIER) cc_final: 0.8654 (p) REVERT: A 465 SER cc_start: 0.9294 (t) cc_final: 0.8943 (m) REVERT: A 479 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7677 (mp) REVERT: A 506 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8505 (tt) REVERT: A 522 MET cc_start: 0.8853 (mmp) cc_final: 0.8313 (mmp) REVERT: A 524 ASP cc_start: 0.8979 (t0) cc_final: 0.8776 (t70) REVERT: A 584 TYR cc_start: 0.8580 (m-10) cc_final: 0.8197 (m-10) REVERT: A 644 MET cc_start: 0.7662 (mmm) cc_final: 0.6135 (tmm) REVERT: A 688 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7692 (mm-30) REVERT: B 14 ASN cc_start: 0.9086 (OUTLIER) cc_final: 0.8733 (t0) REVERT: B 42 TRP cc_start: 0.8246 (m100) cc_final: 0.7630 (m100) REVERT: B 82 MET cc_start: 0.8539 (tpp) cc_final: 0.8162 (ttt) REVERT: B 86 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8286 (mt-10) REVERT: B 121 VAL cc_start: 0.5246 (OUTLIER) cc_final: 0.4948 (p) REVERT: B 169 PHE cc_start: 0.7339 (m-80) cc_final: 0.7115 (m-80) REVERT: B 226 LEU cc_start: 0.9195 (mt) cc_final: 0.8853 (mt) REVERT: B 303 SER cc_start: 0.9105 (t) cc_final: 0.8889 (p) REVERT: B 326 VAL cc_start: 0.9060 (t) cc_final: 0.8857 (p) REVERT: B 344 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.7905 (ttm110) REVERT: B 360 ILE cc_start: 0.9041 (pp) cc_final: 0.8828 (pp) REVERT: B 361 TYR cc_start: 0.8662 (t80) cc_final: 0.8052 (t80) REVERT: B 363 PRO cc_start: 0.9327 (Cg_exo) cc_final: 0.8949 (Cg_endo) REVERT: B 376 ARG cc_start: 0.8241 (ttm110) cc_final: 0.8016 (mtm-85) REVERT: B 430 LEU cc_start: 0.8266 (tp) cc_final: 0.8041 (tt) REVERT: B 438 PHE cc_start: 0.8951 (m-10) cc_final: 0.8608 (m-10) REVERT: B 441 PHE cc_start: 0.7690 (m-80) cc_final: 0.7426 (m-80) REVERT: B 447 MET cc_start: 0.8980 (tpt) cc_final: 0.8627 (tpp) REVERT: B 460 PHE cc_start: 0.8360 (t80) cc_final: 0.8118 (t80) REVERT: B 465 SER cc_start: 0.9352 (t) cc_final: 0.8994 (m) REVERT: B 479 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7648 (mp) REVERT: B 522 MET cc_start: 0.8748 (mmp) cc_final: 0.8514 (mmp) REVERT: B 571 GLU cc_start: 0.8546 (tp30) cc_final: 0.8135 (tp30) REVERT: B 577 TYR cc_start: 0.7233 (m-80) cc_final: 0.6788 (m-80) REVERT: B 686 LEU cc_start: 0.9505 (mt) cc_final: 0.9301 (mt) outliers start: 51 outliers final: 40 residues processed: 317 average time/residue: 0.0666 time to fit residues: 32.5507 Evaluate side-chains 323 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 275 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 575 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 575 GLN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 673 CYS Chi-restraints excluded: chain B residue 678 GLU Chi-restraints excluded: chain B residue 691 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 90 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 71 optimal weight: 0.0870 chunk 81 optimal weight: 7.9990 chunk 89 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 GLN ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 HIS B 31 GLN B 575 GLN ** B 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.131840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.115332 restraints weight = 18520.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.118747 restraints weight = 8274.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.120855 restraints weight = 4807.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.122176 restraints weight = 3328.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.123053 restraints weight = 2608.562| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9854 Z= 0.152 Angle : 0.724 11.233 13438 Z= 0.356 Chirality : 0.043 0.152 1548 Planarity : 0.005 0.053 1666 Dihedral : 5.703 59.101 1322 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 5.38 % Allowed : 28.99 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.25), residues: 1192 helix: 0.45 (0.18), residues: 826 sheet: -3.65 (1.04), residues: 24 loop : -2.31 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 631 TYR 0.036 0.002 TYR B 577 PHE 0.039 0.001 PHE A 396 TRP 0.036 0.002 TRP B 625 HIS 0.004 0.001 HIS A 608 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 9854) covalent geometry : angle 0.72405 (13438) hydrogen bonds : bond 0.03644 ( 655) hydrogen bonds : angle 4.58951 ( 1959) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 283 time to evaluate : 0.297 Fit side-chains REVERT: A 42 TRP cc_start: 0.8133 (m100) cc_final: 0.7633 (m100) REVERT: A 76 MET cc_start: 0.8014 (tpp) cc_final: 0.7605 (mmm) REVERT: A 115 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9157 (tt) REVERT: A 176 MET cc_start: 0.8533 (tpp) cc_final: 0.8124 (tpp) REVERT: A 226 LEU cc_start: 0.9200 (mt) cc_final: 0.8868 (mt) REVERT: A 247 ASP cc_start: 0.7381 (t70) cc_final: 0.6867 (t0) REVERT: A 260 ASP cc_start: 0.8296 (t70) cc_final: 0.8004 (t70) REVERT: A 296 ILE cc_start: 0.8216 (mm) cc_final: 0.7792 (tp) REVERT: A 361 TYR cc_start: 0.8570 (t80) cc_final: 0.7944 (t80) REVERT: A 363 PRO cc_start: 0.9212 (Cg_exo) cc_final: 0.8775 (Cg_endo) REVERT: A 376 ARG cc_start: 0.8277 (ttm110) cc_final: 0.7993 (mtm-85) REVERT: A 441 PHE cc_start: 0.7646 (m-80) cc_final: 0.7380 (m-80) REVERT: A 452 PHE cc_start: 0.8479 (t80) cc_final: 0.8164 (t80) REVERT: A 465 SER cc_start: 0.9281 (t) cc_final: 0.8926 (m) REVERT: A 479 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7664 (mp) REVERT: A 506 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8511 (tt) REVERT: A 532 GLU cc_start: 0.6289 (tp30) cc_final: 0.5943 (tp30) REVERT: A 644 MET cc_start: 0.7678 (mmm) cc_final: 0.6130 (tmm) REVERT: A 688 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7688 (mm-30) REVERT: B 14 ASN cc_start: 0.9077 (OUTLIER) cc_final: 0.8722 (t0) REVERT: B 82 MET cc_start: 0.8467 (tpp) cc_final: 0.7998 (ttt) REVERT: B 86 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8291 (mt-10) REVERT: B 121 VAL cc_start: 0.5105 (OUTLIER) cc_final: 0.4811 (p) REVERT: B 226 LEU cc_start: 0.9182 (mt) cc_final: 0.8848 (mt) REVERT: B 303 SER cc_start: 0.9089 (t) cc_final: 0.8870 (p) REVERT: B 326 VAL cc_start: 0.9075 (t) cc_final: 0.8874 (p) REVERT: B 344 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7894 (ttm110) REVERT: B 361 TYR cc_start: 0.8648 (t80) cc_final: 0.8047 (t80) REVERT: B 363 PRO cc_start: 0.9312 (Cg_exo) cc_final: 0.8955 (Cg_endo) REVERT: B 376 ARG cc_start: 0.8217 (ttm110) cc_final: 0.7935 (mtm-85) REVERT: B 430 LEU cc_start: 0.8302 (tp) cc_final: 0.8069 (tt) REVERT: B 438 PHE cc_start: 0.8926 (m-10) cc_final: 0.8574 (m-10) REVERT: B 441 PHE cc_start: 0.7672 (m-80) cc_final: 0.7411 (m-80) REVERT: B 447 MET cc_start: 0.8988 (tpt) cc_final: 0.8620 (tpp) REVERT: B 460 PHE cc_start: 0.8264 (t80) cc_final: 0.8048 (t80) REVERT: B 465 SER cc_start: 0.9272 (t) cc_final: 0.8949 (m) REVERT: B 479 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7634 (mp) REVERT: B 522 MET cc_start: 0.8831 (mmp) cc_final: 0.8573 (mmp) REVERT: B 577 TYR cc_start: 0.7417 (m-80) cc_final: 0.6906 (m-80) outliers start: 52 outliers final: 41 residues processed: 306 average time/residue: 0.0682 time to fit residues: 32.2124 Evaluate side-chains 316 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 268 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 575 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 575 GLN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 673 CYS Chi-restraints excluded: chain B residue 678 GLU Chi-restraints excluded: chain B residue 691 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 96 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 31 optimal weight: 0.4980 chunk 117 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 GLN ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN B 575 GLN B 629 HIS ** B 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.132363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.116119 restraints weight = 18501.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.119491 restraints weight = 8226.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.121615 restraints weight = 4768.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.122850 restraints weight = 3281.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.123771 restraints weight = 2584.006| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9854 Z= 0.157 Angle : 0.732 11.348 13438 Z= 0.361 Chirality : 0.044 0.194 1548 Planarity : 0.005 0.053 1666 Dihedral : 5.698 59.467 1322 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 5.18 % Allowed : 29.81 % Favored : 65.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.25), residues: 1192 helix: 0.51 (0.18), residues: 824 sheet: -3.68 (1.02), residues: 24 loop : -2.26 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 45 TYR 0.045 0.002 TYR A 577 PHE 0.038 0.001 PHE A 396 TRP 0.034 0.002 TRP B 625 HIS 0.004 0.001 HIS B 629 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 9854) covalent geometry : angle 0.73196 (13438) hydrogen bonds : bond 0.03746 ( 655) hydrogen bonds : angle 4.60502 ( 1959) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 278 time to evaluate : 0.356 Fit side-chains REVERT: A 42 TRP cc_start: 0.8024 (m100) cc_final: 0.7572 (m100) REVERT: A 176 MET cc_start: 0.8503 (tpp) cc_final: 0.8120 (tpp) REVERT: A 226 LEU cc_start: 0.9184 (mt) cc_final: 0.8877 (mt) REVERT: A 247 ASP cc_start: 0.7294 (t70) cc_final: 0.6784 (t0) REVERT: A 260 ASP cc_start: 0.8238 (t70) cc_final: 0.7942 (t70) REVERT: A 296 ILE cc_start: 0.8170 (mm) cc_final: 0.7741 (tp) REVERT: A 361 TYR cc_start: 0.8646 (t80) cc_final: 0.8075 (t80) REVERT: A 363 PRO cc_start: 0.9180 (Cg_exo) cc_final: 0.8672 (Cg_endo) REVERT: A 376 ARG cc_start: 0.8252 (ttm110) cc_final: 0.7966 (mtm-85) REVERT: A 441 PHE cc_start: 0.7604 (m-80) cc_final: 0.7368 (m-80) REVERT: A 452 PHE cc_start: 0.8390 (t80) cc_final: 0.8158 (t80) REVERT: A 479 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7755 (mp) REVERT: A 506 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8504 (tt) REVERT: A 532 GLU cc_start: 0.6249 (tp30) cc_final: 0.5931 (tp30) REVERT: A 644 MET cc_start: 0.7685 (mmm) cc_final: 0.6173 (tmm) REVERT: A 688 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7668 (mm-30) REVERT: B 14 ASN cc_start: 0.9025 (OUTLIER) cc_final: 0.8686 (t0) REVERT: B 82 MET cc_start: 0.8462 (tpp) cc_final: 0.7914 (ttt) REVERT: B 86 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8237 (mt-10) REVERT: B 121 VAL cc_start: 0.5058 (OUTLIER) cc_final: 0.4778 (p) REVERT: B 226 LEU cc_start: 0.9153 (mt) cc_final: 0.8836 (mt) REVERT: B 303 SER cc_start: 0.9073 (t) cc_final: 0.8866 (p) REVERT: B 344 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7901 (ttm110) REVERT: B 361 TYR cc_start: 0.8633 (t80) cc_final: 0.8034 (t80) REVERT: B 363 PRO cc_start: 0.9235 (Cg_exo) cc_final: 0.8855 (Cg_endo) REVERT: B 376 ARG cc_start: 0.8192 (ttm110) cc_final: 0.7939 (mtm-85) REVERT: B 430 LEU cc_start: 0.8334 (tp) cc_final: 0.8102 (tt) REVERT: B 438 PHE cc_start: 0.8894 (m-10) cc_final: 0.8564 (m-10) REVERT: B 441 PHE cc_start: 0.7621 (m-80) cc_final: 0.7379 (m-80) REVERT: B 447 MET cc_start: 0.8978 (tpt) cc_final: 0.8639 (tpp) REVERT: B 452 PHE cc_start: 0.8677 (t80) cc_final: 0.8350 (t80) REVERT: B 460 PHE cc_start: 0.8317 (t80) cc_final: 0.8101 (t80) REVERT: B 465 SER cc_start: 0.9283 (t) cc_final: 0.8959 (m) REVERT: B 479 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7672 (mp) REVERT: B 522 MET cc_start: 0.8795 (mmp) cc_final: 0.8578 (mmp) REVERT: B 577 TYR cc_start: 0.7417 (m-80) cc_final: 0.6990 (m-80) REVERT: B 629 HIS cc_start: 0.8152 (t70) cc_final: 0.7924 (t70) outliers start: 50 outliers final: 41 residues processed: 301 average time/residue: 0.0651 time to fit residues: 30.5767 Evaluate side-chains 316 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 269 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 575 GLN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 673 CYS Chi-restraints excluded: chain B residue 678 GLU Chi-restraints excluded: chain B residue 691 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 23 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 8 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 GLN ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN B 575 GLN ** B 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.133316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.117196 restraints weight = 18389.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.120557 restraints weight = 8240.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.122683 restraints weight = 4774.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.124007 restraints weight = 3273.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.124873 restraints weight = 2543.782| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9854 Z= 0.153 Angle : 0.736 11.308 13438 Z= 0.362 Chirality : 0.043 0.142 1548 Planarity : 0.005 0.052 1666 Dihedral : 5.763 59.829 1322 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 4.97 % Allowed : 30.12 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.25), residues: 1192 helix: 0.53 (0.18), residues: 824 sheet: -3.52 (1.01), residues: 24 loop : -2.26 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 631 TYR 0.037 0.002 TYR B 577 PHE 0.041 0.001 PHE A 396 TRP 0.030 0.002 TRP B 625 HIS 0.005 0.001 HIS A 608 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9854) covalent geometry : angle 0.73640 (13438) hydrogen bonds : bond 0.03659 ( 655) hydrogen bonds : angle 4.62187 ( 1959) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1681.29 seconds wall clock time: 29 minutes 46.30 seconds (1786.30 seconds total)