Starting phenix.real_space_refine on Fri Mar 14 06:22:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jpf_6822/03_2025/6jpf_6822.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jpf_6822/03_2025/6jpf_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6jpf_6822/03_2025/6jpf_6822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jpf_6822/03_2025/6jpf_6822.map" model { file = "/net/cci-nas-00/data/ceres_data/6jpf_6822/03_2025/6jpf_6822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jpf_6822/03_2025/6jpf_6822.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 4, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 90 Restraints were copied for chains: B Time building chain proxies: 8.78, per 1000 atoms: 0.92 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: 2.56 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.00 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: 2.86 Time building geometry restraints manager: 3.01 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.520 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.120 ------------------------------------------------------------------------------- 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= 0.298 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.022 0.002 TRP B 625 HIS 0.009 0.002 HIS B 608 PHE 0.017 0.002 PHE B 669 TYR 0.028 0.002 TYR B 181 ARG 0.004 0.001 ARG A 331 *********************** 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 : 1.037 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: 0.1948 time to fit residues: 117.1586 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 : 1.101 ------------------------------------------------------------------------------- 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 103 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 0.1980 chunk 110 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.121986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.104322 restraints weight = 18686.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.107583 restraints weight = 8246.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.109704 restraints weight = 4830.917| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9854 Z= 0.247 Angle : 0.736 8.299 13438 Z= 0.371 Chirality : 0.044 0.168 1548 Planarity : 0.006 0.066 1666 Dihedral : 7.477 56.745 1342 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 6.00 % Allowed : 19.57 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.23), residues: 1192 helix: -0.71 (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 TRP 0.020 0.002 TRP A 625 HIS 0.005 0.001 HIS B 608 PHE 0.042 0.002 PHE B 21 TYR 0.020 0.002 TYR B 181 ARG 0.005 0.001 ARG B 683 *********************** 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 : 1.187 Fit side-chains REVERT: A 17 THR cc_start: 0.9273 (m) cc_final: 0.8590 (t) REVERT: A 30 LEU cc_start: 0.8857 (mt) cc_final: 0.8539 (pp) REVERT: A 36 ARG cc_start: 0.8993 (mtp180) cc_final: 0.8616 (ttm-80) REVERT: A 115 LEU cc_start: 0.9368 (tt) cc_final: 0.9081 (tt) REVERT: A 176 MET cc_start: 0.8354 (tpp) cc_final: 0.7965 (tpp) REVERT: A 201 GLN cc_start: 0.8638 (mt0) cc_final: 0.8215 (mp10) REVERT: A 208 ASN cc_start: 0.8191 (m-40) cc_final: 0.7937 (m-40) REVERT: A 226 LEU cc_start: 0.9262 (mt) cc_final: 0.8873 (mt) REVERT: A 247 ASP cc_start: 0.7562 (t70) cc_final: 0.7118 (t0) REVERT: A 257 ASN cc_start: 0.9070 (p0) cc_final: 0.8776 (m-40) REVERT: A 260 ASP cc_start: 0.8520 (m-30) cc_final: 0.8311 (t70) REVERT: A 360 ILE cc_start: 0.9108 (pt) cc_final: 0.8888 (pt) REVERT: A 361 TYR cc_start: 0.8555 (t80) cc_final: 0.7764 (t80) REVERT: A 363 PRO cc_start: 0.9358 (Cg_exo) cc_final: 0.8793 (Cg_endo) REVERT: A 376 ARG cc_start: 0.8347 (ttm110) cc_final: 0.8129 (mtm-85) REVERT: A 438 PHE cc_start: 0.8794 (m-10) cc_final: 0.8471 (m-10) REVERT: A 441 PHE cc_start: 0.7896 (m-80) cc_final: 0.7595 (m-80) REVERT: A 460 PHE cc_start: 0.8334 (t80) cc_final: 0.8128 (t80) REVERT: A 465 SER cc_start: 0.9286 (t) cc_final: 0.9000 (m) REVERT: A 479 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7613 (mp) REVERT: A 524 ASP cc_start: 0.9025 (t0) cc_final: 0.8794 (t70) REVERT: A 688 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8169 (mm-30) REVERT: B 30 LEU cc_start: 0.8860 (mt) cc_final: 0.8556 (pp) REVERT: B 36 ARG cc_start: 0.8601 (mmm160) cc_final: 0.8351 (mmm160) REVERT: B 94 ASP cc_start: 0.8031 (p0) cc_final: 0.7633 (p0) REVERT: B 115 LEU cc_start: 0.9361 (tt) cc_final: 0.8900 (tt) REVERT: B 208 ASN cc_start: 0.8265 (m-40) cc_final: 0.7985 (m-40) REVERT: B 226 LEU cc_start: 0.9206 (mt) cc_final: 0.8875 (mt) REVERT: B 247 ASP cc_start: 0.7548 (t70) cc_final: 0.7239 (t0) REVERT: B 257 ASN cc_start: 0.8449 (m-40) cc_final: 0.8076 (p0) REVERT: B 260 ASP cc_start: 0.8509 (m-30) cc_final: 0.8125 (t0) REVERT: B 344 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8179 (ttm110) REVERT: B 360 ILE cc_start: 0.9092 (pt) cc_final: 0.8832 (pt) REVERT: B 361 TYR cc_start: 0.8616 (t80) cc_final: 0.8375 (t80) REVERT: B 376 ARG cc_start: 0.8266 (ttm110) cc_final: 0.8045 (mtm-85) REVERT: B 430 LEU cc_start: 0.8097 (tp) cc_final: 0.7817 (tt) REVERT: B 438 PHE cc_start: 0.8951 (m-10) cc_final: 0.8620 (m-10) REVERT: B 441 PHE cc_start: 0.8009 (m-80) cc_final: 0.7684 (m-80) REVERT: B 479 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7451 (mp) REVERT: B 522 MET cc_start: 0.8642 (mmm) cc_final: 0.7879 (mmp) REVERT: B 565 ILE cc_start: 0.9169 (tp) cc_final: 0.8884 (tp) REVERT: B 633 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8663 (tp) REVERT: B 644 MET cc_start: 0.7391 (mtp) cc_final: 0.7156 (tmm) REVERT: B 686 LEU cc_start: 0.9492 (mt) cc_final: 0.9243 (mt) outliers start: 58 outliers final: 27 residues processed: 376 average time/residue: 0.1754 time to fit residues: 96.8056 Evaluate side-chains 331 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 300 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 A residue 646 LEU 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 51 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.3565 r_free = 0.3565 target = 0.120258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.102287 restraints weight = 18746.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.105548 restraints weight = 8481.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.107663 restraints weight = 5078.704| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 9854 Z= 0.359 Angle : 0.742 8.907 13438 Z= 0.381 Chirality : 0.046 0.169 1548 Planarity : 0.005 0.059 1666 Dihedral : 6.587 57.285 1332 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 6.31 % Allowed : 21.74 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.24), residues: 1192 helix: -0.35 (0.17), residues: 858 sheet: -3.85 (0.89), residues: 24 loop : -2.79 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 625 HIS 0.004 0.001 HIS B 294 PHE 0.020 0.002 PHE B 598 TYR 0.018 0.002 TYR A 181 ARG 0.006 0.001 ARG A 344 *********************** 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 364 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 303 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 PHE cc_start: 0.8859 (m-80) cc_final: 0.8410 (m-80) REVERT: A 36 ARG cc_start: 0.8984 (mtp180) cc_final: 0.8679 (tpp80) REVERT: A 76 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.8014 (tpp) REVERT: A 115 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9018 (tt) REVERT: A 176 MET cc_start: 0.8447 (tpp) cc_final: 0.8010 (tpp) REVERT: A 361 TYR cc_start: 0.8817 (t80) cc_final: 0.8143 (t80) REVERT: A 363 PRO cc_start: 0.9408 (Cg_exo) cc_final: 0.9039 (Cg_endo) REVERT: A 438 PHE cc_start: 0.8897 (m-10) cc_final: 0.8520 (m-10) REVERT: A 441 PHE cc_start: 0.7807 (m-80) cc_final: 0.7451 (m-80) REVERT: A 460 PHE cc_start: 0.8436 (t80) cc_final: 0.8210 (t80) REVERT: A 461 LEU cc_start: 0.9143 (tt) cc_final: 0.8924 (tp) REVERT: A 465 SER cc_start: 0.9296 (t) cc_final: 0.8975 (m) REVERT: A 479 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7788 (mp) REVERT: A 522 MET cc_start: 0.8687 (mmm) cc_final: 0.7569 (mmp) REVERT: A 524 ASP cc_start: 0.9001 (t0) cc_final: 0.8741 (t70) REVERT: A 526 TRP cc_start: 0.8459 (m-10) cc_final: 0.8177 (m-10) REVERT: A 688 GLU cc_start: 0.8591 (mm-30) cc_final: 0.7911 (mm-30) REVERT: B 21 PHE cc_start: 0.8792 (m-80) cc_final: 0.8411 (m-80) REVERT: B 115 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9078 (tt) REVERT: B 176 MET cc_start: 0.8342 (tpp) cc_final: 0.8025 (tpp) REVERT: B 201 GLN cc_start: 0.8511 (mt0) cc_final: 0.8242 (mp10) REVERT: B 226 LEU cc_start: 0.9200 (mt) cc_final: 0.8875 (mt) REVERT: B 247 ASP cc_start: 0.7381 (t70) cc_final: 0.7039 (t0) REVERT: B 344 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8151 (ttm110) REVERT: B 361 TYR cc_start: 0.8858 (t80) cc_final: 0.8151 (t80) REVERT: B 363 PRO cc_start: 0.9428 (Cg_exo) cc_final: 0.9021 (Cg_endo) REVERT: B 376 ARG cc_start: 0.8323 (ttm110) cc_final: 0.8070 (mtm-85) REVERT: B 430 LEU cc_start: 0.8099 (tp) cc_final: 0.7839 (tt) REVERT: B 441 PHE cc_start: 0.7915 (m-80) cc_final: 0.7581 (m-80) REVERT: B 447 MET cc_start: 0.9104 (tpt) cc_final: 0.8810 (tpp) REVERT: B 479 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7625 (mp) REVERT: B 522 MET cc_start: 0.8639 (mmm) cc_final: 0.8401 (tpp) REVERT: B 524 ASP cc_start: 0.9072 (t0) cc_final: 0.8762 (t70) REVERT: B 616 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7794 (mm-40) REVERT: B 644 MET cc_start: 0.7353 (mtp) cc_final: 0.7050 (tmm) REVERT: B 686 LEU cc_start: 0.9521 (mt) cc_final: 0.9302 (mt) outliers start: 61 outliers final: 36 residues processed: 332 average time/residue: 0.1558 time to fit residues: 78.6506 Evaluate side-chains 322 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 280 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL 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 120 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 390 PHE 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 588 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 120 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 306 ILE 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 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 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 691 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 109 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 GLN ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** B 616 GLN ** 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 = 0.3609 r_free = 0.3609 target = 0.123556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.105956 restraints weight = 18389.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.109222 restraints weight = 8292.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.111327 restraints weight = 4921.463| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9854 Z= 0.264 Angle : 0.706 9.720 13438 Z= 0.356 Chirality : 0.043 0.176 1548 Planarity : 0.005 0.058 1666 Dihedral : 6.287 53.010 1328 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 6.00 % Allowed : 24.12 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.24), residues: 1192 helix: -0.07 (0.17), residues: 852 sheet: -3.93 (0.92), residues: 24 loop : -2.54 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 625 HIS 0.005 0.001 HIS A 608 PHE 0.019 0.002 PHE A 72 TYR 0.017 0.002 TYR A 102 ARG 0.004 0.001 ARG B 468 *********************** 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 370 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 312 time to evaluate : 1.140 Fit side-chains REVERT: A 21 PHE cc_start: 0.8787 (m-80) cc_final: 0.8067 (m-80) REVERT: A 30 LEU cc_start: 0.8847 (mt) cc_final: 0.8546 (pp) REVERT: A 36 ARG cc_start: 0.8967 (mtp180) cc_final: 0.8402 (ttm170) REVERT: A 115 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9107 (tt) REVERT: A 176 MET cc_start: 0.8360 (tpp) cc_final: 0.7949 (tpp) REVERT: A 201 GLN cc_start: 0.8402 (mt0) cc_final: 0.8201 (mp10) REVERT: A 361 TYR cc_start: 0.8741 (t80) cc_final: 0.8073 (t80) REVERT: A 363 PRO cc_start: 0.9347 (Cg_exo) cc_final: 0.9014 (Cg_endo) REVERT: A 438 PHE cc_start: 0.8878 (m-10) cc_final: 0.8487 (m-10) REVERT: A 441 PHE cc_start: 0.7733 (m-80) cc_final: 0.7436 (m-80) REVERT: A 452 PHE cc_start: 0.9036 (t80) cc_final: 0.8153 (t80) REVERT: A 465 SER cc_start: 0.9307 (t) cc_final: 0.8980 (m) REVERT: A 479 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7590 (mp) REVERT: A 524 ASP cc_start: 0.9078 (t0) cc_final: 0.8792 (t70) REVERT: A 640 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8447 (mm-40) REVERT: A 688 GLU cc_start: 0.8428 (mm-30) cc_final: 0.7724 (mm-30) REVERT: B 21 PHE cc_start: 0.8731 (m-80) cc_final: 0.8037 (m-80) REVERT: B 30 LEU cc_start: 0.8819 (mt) cc_final: 0.8552 (pp) REVERT: B 94 ASP cc_start: 0.7878 (p0) cc_final: 0.7590 (p0) REVERT: B 115 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9070 (tt) REVERT: B 176 MET cc_start: 0.8336 (tpp) cc_final: 0.7942 (tpp) REVERT: B 226 LEU cc_start: 0.9169 (mt) cc_final: 0.8911 (mt) REVERT: B 247 ASP cc_start: 0.7194 (t70) cc_final: 0.6843 (t0) REVERT: B 336 VAL cc_start: 0.8899 (OUTLIER) cc_final: 0.8689 (p) REVERT: B 344 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8073 (ttm110) REVERT: B 361 TYR cc_start: 0.8768 (t80) cc_final: 0.8098 (t80) REVERT: B 363 PRO cc_start: 0.9386 (Cg_exo) cc_final: 0.8971 (Cg_endo) REVERT: B 430 LEU cc_start: 0.8151 (tp) cc_final: 0.7931 (tt) REVERT: B 441 PHE cc_start: 0.7868 (m-80) cc_final: 0.7515 (m-80) REVERT: B 447 MET cc_start: 0.9096 (tpt) cc_final: 0.8772 (tpp) REVERT: B 522 MET cc_start: 0.8625 (mmm) cc_final: 0.7491 (mmp) REVERT: B 524 ASP cc_start: 0.9123 (t0) cc_final: 0.8763 (t70) REVERT: B 526 TRP cc_start: 0.8547 (m-10) cc_final: 0.8082 (m-10) REVERT: B 644 MET cc_start: 0.7182 (mtp) cc_final: 0.6942 (tmm) REVERT: B 686 LEU cc_start: 0.9513 (mt) cc_final: 0.9266 (mt) outliers start: 58 outliers final: 39 residues processed: 338 average time/residue: 0.1746 time to fit residues: 89.8859 Evaluate side-chains 325 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 281 time to evaluate : 1.146 ------------------------------------------------------------------------------- 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 171 ILE 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 259 LEU Chi-restraints excluded: chain A residue 260 ASP 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 482 VAL Chi-restraints excluded: chain A residue 510 ILE 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 9 VAL 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 306 ILE 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 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 646 LEU 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 80 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 91 optimal weight: 0.0370 chunk 99 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- 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 608 HIS ** 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 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** B 608 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 = 0.3656 r_free = 0.3656 target = 0.126668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.109029 restraints weight = 18166.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.112308 restraints weight = 8310.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.114416 restraints weight = 4953.834| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9854 Z= 0.233 Angle : 0.704 9.901 13438 Z= 0.354 Chirality : 0.043 0.173 1548 Planarity : 0.005 0.056 1666 Dihedral : 6.022 50.869 1326 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 5.59 % Allowed : 25.05 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.25), residues: 1192 helix: 0.17 (0.18), residues: 824 sheet: -3.99 (0.94), residues: 24 loop : -2.13 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 75 HIS 0.005 0.001 HIS B 608 PHE 0.017 0.002 PHE B 669 TYR 0.023 0.002 TYR B 102 ARG 0.004 0.001 ARG B 197 *********************** 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 371 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 317 time to evaluate : 1.176 Fit side-chains revert: symmetry clash REVERT: A 21 PHE cc_start: 0.8643 (m-80) cc_final: 0.7945 (m-80) REVERT: A 30 LEU cc_start: 0.8861 (mt) cc_final: 0.8600 (pp) REVERT: A 75 TRP cc_start: 0.7877 (t60) cc_final: 0.7606 (t60) REVERT: A 115 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.8943 (tt) REVERT: A 176 MET cc_start: 0.8367 (tpp) cc_final: 0.8028 (tpp) REVERT: A 247 ASP cc_start: 0.7575 (t70) cc_final: 0.7081 (t0) REVERT: A 361 TYR cc_start: 0.8658 (t80) cc_final: 0.8071 (t80) REVERT: A 363 PRO cc_start: 0.9274 (Cg_exo) cc_final: 0.8979 (Cg_endo) REVERT: A 438 PHE cc_start: 0.8857 (m-10) cc_final: 0.8480 (m-10) REVERT: A 441 PHE cc_start: 0.7707 (m-80) cc_final: 0.7379 (m-80) REVERT: A 465 SER cc_start: 0.9335 (t) cc_final: 0.8951 (m) REVERT: A 479 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7651 (mp) REVERT: A 522 MET cc_start: 0.8864 (mmp) cc_final: 0.8494 (mmp) REVERT: A 524 ASP cc_start: 0.9036 (t0) cc_final: 0.8611 (t70) REVERT: A 526 TRP cc_start: 0.8331 (m-10) cc_final: 0.7913 (m-10) REVERT: A 644 MET cc_start: 0.7598 (mmm) cc_final: 0.6651 (tmm) REVERT: A 688 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7749 (mm-30) REVERT: B 30 LEU cc_start: 0.8759 (mt) cc_final: 0.8546 (pp) REVERT: B 115 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.8956 (tt) REVERT: B 176 MET cc_start: 0.8320 (tpp) cc_final: 0.8000 (tpp) REVERT: B 226 LEU cc_start: 0.9150 (mt) cc_final: 0.8888 (mt) REVERT: B 344 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8086 (ttm110) REVERT: B 361 TYR cc_start: 0.8668 (t80) cc_final: 0.8034 (t80) REVERT: B 363 PRO cc_start: 0.9330 (Cg_exo) cc_final: 0.8968 (Cg_endo) REVERT: B 430 LEU cc_start: 0.8299 (tp) cc_final: 0.8087 (tt) REVERT: B 438 PHE cc_start: 0.8992 (m-10) cc_final: 0.8637 (m-10) REVERT: B 441 PHE cc_start: 0.7789 (m-80) cc_final: 0.7549 (m-80) REVERT: B 447 MET cc_start: 0.9143 (tpt) cc_final: 0.8813 (tpp) REVERT: B 479 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7578 (mp) REVERT: B 522 MET cc_start: 0.8543 (mmm) cc_final: 0.8006 (mmp) REVERT: B 524 ASP cc_start: 0.9098 (t0) cc_final: 0.8781 (t70) REVERT: B 526 TRP cc_start: 0.8473 (m-10) cc_final: 0.8202 (m-10) REVERT: B 532 GLU cc_start: 0.6527 (tp30) cc_final: 0.6313 (tp30) REVERT: B 686 LEU cc_start: 0.9491 (mt) cc_final: 0.9271 (mt) outliers start: 54 outliers final: 38 residues processed: 340 average time/residue: 0.1701 time to fit residues: 86.2282 Evaluate side-chains 328 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 285 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 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 260 ASP 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 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 539 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 120 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.122662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.105053 restraints weight = 18407.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.108271 restraints weight = 8361.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110368 restraints weight = 4987.956| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 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 : 0.005 0.052 9854 Z= 0.341 Angle : 0.756 10.192 13438 Z= 0.378 Chirality : 0.046 0.178 1548 Planarity : 0.005 0.057 1666 Dihedral : 5.796 44.035 1322 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 5.49 % Allowed : 27.23 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.24), residues: 1192 helix: 0.22 (0.18), residues: 830 sheet: -3.83 (1.04), residues: 24 loop : -2.38 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 625 HIS 0.004 0.001 HIS B 608 PHE 0.030 0.002 PHE A 396 TYR 0.041 0.002 TYR B 577 ARG 0.011 0.001 ARG B 197 *********************** 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 337 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 284 time to evaluate : 0.982 Fit side-chains REVERT: A 30 LEU cc_start: 0.8923 (mt) cc_final: 0.8613 (pp) REVERT: A 115 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9083 (tt) REVERT: A 361 TYR cc_start: 0.8751 (t80) cc_final: 0.8116 (t80) REVERT: A 363 PRO cc_start: 0.9399 (Cg_exo) cc_final: 0.9080 (Cg_endo) REVERT: A 441 PHE cc_start: 0.7690 (m-80) cc_final: 0.7367 (m-80) REVERT: A 479 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7807 (mp) REVERT: A 506 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8528 (pp) REVERT: A 510 ILE cc_start: 0.7585 (OUTLIER) cc_final: 0.7206 (mt) REVERT: A 522 MET cc_start: 0.8791 (mmp) cc_final: 0.8250 (mmp) REVERT: A 524 ASP cc_start: 0.9113 (t0) cc_final: 0.8802 (t70) REVERT: A 526 TRP cc_start: 0.8298 (m-10) cc_final: 0.7757 (m-10) REVERT: A 644 MET cc_start: 0.7825 (mmm) cc_final: 0.6419 (tmm) REVERT: A 688 GLU cc_start: 0.8447 (mm-30) cc_final: 0.7755 (mm-30) REVERT: B 30 LEU cc_start: 0.8858 (mt) cc_final: 0.8566 (pp) REVERT: B 115 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9107 (tt) REVERT: B 344 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8055 (ttm110) REVERT: B 361 TYR cc_start: 0.8805 (t80) cc_final: 0.8157 (t80) REVERT: B 363 PRO cc_start: 0.9384 (Cg_exo) cc_final: 0.9089 (Cg_endo) REVERT: B 430 LEU cc_start: 0.8256 (tp) cc_final: 0.7931 (tt) REVERT: B 438 PHE cc_start: 0.8995 (m-10) cc_final: 0.8611 (m-10) REVERT: B 441 PHE cc_start: 0.7862 (m-80) cc_final: 0.7586 (m-80) REVERT: B 447 MET cc_start: 0.9058 (tpt) cc_final: 0.8491 (tpp) REVERT: B 479 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7664 (mp) REVERT: B 522 MET cc_start: 0.8621 (mmm) cc_final: 0.7923 (mmp) REVERT: B 524 ASP cc_start: 0.9155 (t0) cc_final: 0.8866 (t70) REVERT: B 526 TRP cc_start: 0.8477 (m-10) cc_final: 0.8109 (m-10) REVERT: B 577 TYR cc_start: 0.7744 (m-80) cc_final: 0.7325 (m-80) REVERT: B 686 LEU cc_start: 0.9505 (mt) cc_final: 0.9268 (mt) outliers start: 53 outliers final: 42 residues processed: 306 average time/residue: 0.1503 time to fit residues: 70.7105 Evaluate side-chains 320 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 271 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 120 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 217 VAL 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 260 ASP Chi-restraints excluded: chain A residue 386 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 482 VAL 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 673 CYS Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 714 ILE 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 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 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 678 GLU Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 714 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 91 optimal weight: 0.0670 chunk 52 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 89 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 608 HIS ** 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 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.128936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.111778 restraints weight = 18378.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.115144 restraints weight = 8218.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.117265 restraints weight = 4801.402| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4471 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= 0.226 Angle : 0.729 10.836 13438 Z= 0.360 Chirality : 0.044 0.172 1548 Planarity : 0.005 0.054 1666 Dihedral : 5.790 57.724 1322 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 5.69 % Allowed : 29.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.25), residues: 1192 helix: 0.31 (0.18), residues: 818 sheet: -3.77 (1.01), residues: 24 loop : -2.17 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 625 HIS 0.005 0.001 HIS B 608 PHE 0.025 0.002 PHE A 396 TYR 0.035 0.002 TYR A 102 ARG 0.009 0.001 ARG B 197 *********************** 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 361 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 306 time to evaluate : 1.285 Fit side-chains REVERT: A 75 TRP cc_start: 0.7818 (t60) cc_final: 0.7322 (t60) REVERT: A 76 MET cc_start: 0.8186 (tpp) cc_final: 0.7673 (tpp) REVERT: A 115 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9090 (tt) REVERT: A 176 MET cc_start: 0.8478 (tpp) cc_final: 0.8018 (tpp) REVERT: A 247 ASP cc_start: 0.7434 (t70) cc_final: 0.6931 (t0) REVERT: A 361 TYR cc_start: 0.8698 (t80) cc_final: 0.8073 (t80) REVERT: A 363 PRO cc_start: 0.9315 (Cg_exo) cc_final: 0.8969 (Cg_endo) REVERT: A 441 PHE cc_start: 0.7561 (m-80) cc_final: 0.7245 (m-80) REVERT: A 460 PHE cc_start: 0.8394 (t80) cc_final: 0.8170 (t80) REVERT: A 479 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7652 (mp) REVERT: A 522 MET cc_start: 0.8733 (mmp) cc_final: 0.8160 (mmp) REVERT: A 524 ASP cc_start: 0.8984 (t0) cc_final: 0.8562 (t70) REVERT: A 526 TRP cc_start: 0.8214 (m-10) cc_final: 0.7632 (m-10) REVERT: A 644 MET cc_start: 0.7749 (mmm) cc_final: 0.6308 (tmm) REVERT: A 688 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7677 (mm-30) REVERT: B 197 ARG cc_start: 0.7553 (ttm110) cc_final: 0.7330 (ttm110) REVERT: B 344 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8051 (ttm110) REVERT: B 361 TYR cc_start: 0.8670 (t80) cc_final: 0.8041 (t80) REVERT: B 363 PRO cc_start: 0.9306 (Cg_exo) cc_final: 0.9061 (Cg_endo) REVERT: B 430 LEU cc_start: 0.8301 (tp) cc_final: 0.8065 (tt) REVERT: B 438 PHE cc_start: 0.8972 (m-10) cc_final: 0.8606 (m-10) REVERT: B 441 PHE cc_start: 0.7720 (m-80) cc_final: 0.7464 (m-80) REVERT: B 447 MET cc_start: 0.9016 (tpt) cc_final: 0.8531 (tpp) REVERT: B 452 PHE cc_start: 0.8866 (t80) cc_final: 0.8378 (t80) REVERT: B 479 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7587 (mp) REVERT: B 522 MET cc_start: 0.8579 (mmm) cc_final: 0.7983 (mmp) REVERT: B 524 ASP cc_start: 0.9039 (t0) cc_final: 0.8705 (t70) REVERT: B 526 TRP cc_start: 0.8299 (m-10) cc_final: 0.8095 (m-10) REVERT: B 577 TYR cc_start: 0.7636 (m-80) cc_final: 0.7323 (m-80) REVERT: B 686 LEU cc_start: 0.9464 (mt) cc_final: 0.9221 (mt) outliers start: 55 outliers final: 44 residues processed: 333 average time/residue: 0.1848 time to fit residues: 92.0571 Evaluate side-chains 328 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 280 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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 217 VAL 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 260 ASP 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 482 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 539 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 A residue 673 CYS Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 217 VAL 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 539 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 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 60 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 10 optimal weight: 0.3980 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 104 optimal weight: 0.0870 chunk 27 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 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 = 0.3719 r_free = 0.3719 target = 0.131478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.114554 restraints weight = 18389.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.117974 restraints weight = 8233.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.120159 restraints weight = 4787.065| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9854 Z= 0.221 Angle : 0.758 12.222 13438 Z= 0.367 Chirality : 0.045 0.268 1548 Planarity : 0.005 0.053 1666 Dihedral : 5.716 56.696 1322 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 5.59 % Allowed : 29.09 % Favored : 65.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.25), residues: 1192 helix: 0.38 (0.18), residues: 822 sheet: -3.69 (1.01), residues: 24 loop : -2.29 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 625 HIS 0.004 0.001 HIS A 608 PHE 0.022 0.002 PHE A 396 TYR 0.022 0.002 TYR B 577 ARG 0.007 0.001 ARG B 197 *********************** 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 352 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 298 time to evaluate : 0.994 Fit side-chains REVERT: A 115 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9050 (tt) REVERT: A 176 MET cc_start: 0.8481 (tpp) cc_final: 0.8053 (tpp) REVERT: A 247 ASP cc_start: 0.7425 (t70) cc_final: 0.6927 (t0) REVERT: A 258 TRP cc_start: 0.8323 (m100) cc_final: 0.8068 (m100) REVERT: A 361 TYR cc_start: 0.8654 (t80) cc_final: 0.8014 (t80) REVERT: A 363 PRO cc_start: 0.9198 (Cg_exo) cc_final: 0.8763 (Cg_endo) REVERT: A 441 PHE cc_start: 0.7532 (m-80) cc_final: 0.7173 (m-80) REVERT: A 460 PHE cc_start: 0.8322 (t80) cc_final: 0.8067 (t80) REVERT: A 479 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7712 (mp) REVERT: A 522 MET cc_start: 0.8688 (mmp) cc_final: 0.8137 (mmp) REVERT: A 524 ASP cc_start: 0.8962 (t0) cc_final: 0.8752 (t70) REVERT: A 526 TRP cc_start: 0.8159 (m-10) cc_final: 0.7536 (m-10) REVERT: A 640 GLN cc_start: 0.8707 (mm-40) cc_final: 0.8446 (mm-40) REVERT: A 688 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7548 (mm-30) REVERT: B 42 TRP cc_start: 0.8345 (m100) cc_final: 0.7784 (m100) REVERT: B 197 ARG cc_start: 0.7575 (ttm110) cc_final: 0.7308 (ttm110) REVERT: B 226 LEU cc_start: 0.9106 (mt) cc_final: 0.8698 (mt) REVERT: B 344 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7949 (ttm110) REVERT: B 361 TYR cc_start: 0.8611 (t80) cc_final: 0.7990 (t80) REVERT: B 363 PRO cc_start: 0.9309 (Cg_exo) cc_final: 0.8989 (Cg_endo) REVERT: B 430 LEU cc_start: 0.8345 (tp) cc_final: 0.8118 (tt) REVERT: B 438 PHE cc_start: 0.8959 (m-10) cc_final: 0.8614 (m-10) REVERT: B 441 PHE cc_start: 0.7687 (m-80) cc_final: 0.7409 (m-80) REVERT: B 447 MET cc_start: 0.8962 (tpt) cc_final: 0.8556 (tpp) REVERT: B 479 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7578 (mp) REVERT: B 524 ASP cc_start: 0.9042 (t0) cc_final: 0.8723 (t70) REVERT: B 686 LEU cc_start: 0.9441 (mt) cc_final: 0.9219 (mt) outliers start: 54 outliers final: 38 residues processed: 324 average time/residue: 0.1947 time to fit residues: 94.8450 Evaluate side-chains 316 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 274 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 217 VAL 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 260 ASP 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 539 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 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 162 HIS Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 217 VAL 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 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 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 85 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 73 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 575 GLN ** A 608 HIS ** 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 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 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 = 0.3733 r_free = 0.3733 target = 0.132439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.116066 restraints weight = 18236.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.119453 restraints weight = 8123.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.121603 restraints weight = 4685.366| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9854 Z= 0.241 Angle : 0.787 16.077 13438 Z= 0.381 Chirality : 0.045 0.269 1548 Planarity : 0.005 0.052 1666 Dihedral : 5.648 55.332 1322 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 5.28 % Allowed : 30.12 % Favored : 64.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.25), residues: 1192 helix: 0.44 (0.18), residues: 818 sheet: -3.74 (1.00), residues: 24 loop : -2.36 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 625 HIS 0.005 0.001 HIS A 608 PHE 0.029 0.002 PHE A 396 TYR 0.049 0.002 TYR B 577 ARG 0.006 0.001 ARG B 197 *********************** 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 337 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 286 time to evaluate : 1.128 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.8447 (tpp) cc_final: 0.8024 (tpp) REVERT: A 247 ASP cc_start: 0.7416 (t70) cc_final: 0.6916 (t0) REVERT: A 258 TRP cc_start: 0.8309 (m100) cc_final: 0.8055 (m100) REVERT: A 361 TYR cc_start: 0.8614 (t80) cc_final: 0.7972 (t80) REVERT: A 363 PRO cc_start: 0.9208 (Cg_exo) cc_final: 0.8857 (Cg_endo) REVERT: A 441 PHE cc_start: 0.7512 (m-80) cc_final: 0.7130 (m-80) REVERT: A 460 PHE cc_start: 0.8272 (t80) cc_final: 0.8008 (t80) REVERT: A 479 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7737 (mp) REVERT: A 522 MET cc_start: 0.8632 (mmp) cc_final: 0.8192 (mmp) REVERT: A 526 TRP cc_start: 0.8054 (m-10) cc_final: 0.7678 (m-10) REVERT: A 532 GLU cc_start: 0.6347 (tp30) cc_final: 0.6016 (tp30) REVERT: A 644 MET cc_start: 0.7793 (mmm) cc_final: 0.6297 (tmm) REVERT: A 688 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7565 (mm-30) REVERT: B 42 TRP cc_start: 0.8291 (m100) cc_final: 0.7755 (m100) REVERT: B 197 ARG cc_start: 0.7512 (ttm110) cc_final: 0.7252 (ttm110) REVERT: B 327 SER cc_start: 0.8983 (m) cc_final: 0.8720 (t) REVERT: B 344 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7954 (ttm110) REVERT: B 361 TYR cc_start: 0.8676 (t80) cc_final: 0.8067 (t80) REVERT: B 363 PRO cc_start: 0.9318 (Cg_exo) cc_final: 0.8941 (Cg_endo) REVERT: B 430 LEU cc_start: 0.8327 (tp) cc_final: 0.8107 (tt) REVERT: B 438 PHE cc_start: 0.8939 (m-10) cc_final: 0.8599 (m-10) REVERT: B 441 PHE cc_start: 0.7685 (m-80) cc_final: 0.7402 (m-80) REVERT: B 447 MET cc_start: 0.9023 (tpt) cc_final: 0.8496 (tpp) REVERT: B 479 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7648 (mp) REVERT: B 686 LEU cc_start: 0.9418 (mt) cc_final: 0.9200 (mt) outliers start: 51 outliers final: 41 residues processed: 312 average time/residue: 0.1672 time to fit residues: 78.9187 Evaluate side-chains 320 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 276 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 170 THR Chi-restraints excluded: chain A residue 217 VAL 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 260 ASP 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 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 539 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 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 162 HIS Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 217 VAL 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 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 565 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 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 6 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 22 optimal weight: 9.9990 chunk 56 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 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 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 HIS ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 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 = 0.3730 r_free = 0.3730 target = 0.132143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.115412 restraints weight = 18304.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.118837 restraints weight = 8225.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.120933 restraints weight = 4772.955| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9854 Z= 0.258 Angle : 0.807 16.817 13438 Z= 0.390 Chirality : 0.046 0.379 1548 Planarity : 0.005 0.052 1666 Dihedral : 5.672 55.990 1322 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 4.24 % Allowed : 31.88 % Favored : 63.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.25), residues: 1192 helix: 0.40 (0.18), residues: 824 sheet: -3.73 (1.01), residues: 24 loop : -2.39 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 625 HIS 0.004 0.001 HIS A 608 PHE 0.030 0.002 PHE A 396 TYR 0.061 0.002 TYR B 577 ARG 0.006 0.001 ARG B 197 ********************** 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 323 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 282 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.8454 (tpp) cc_final: 0.7980 (tpp) REVERT: A 247 ASP cc_start: 0.7436 (t70) cc_final: 0.6955 (t0) REVERT: A 258 TRP cc_start: 0.8320 (m100) cc_final: 0.8060 (m100) REVERT: A 260 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.7954 (t0) REVERT: A 361 TYR cc_start: 0.8572 (t80) cc_final: 0.7939 (t80) REVERT: A 363 PRO cc_start: 0.9211 (Cg_exo) cc_final: 0.8661 (Cg_endo) REVERT: A 460 PHE cc_start: 0.8342 (t80) cc_final: 0.8125 (t80) REVERT: A 478 PHE cc_start: 0.8907 (t80) cc_final: 0.8628 (t80) REVERT: A 522 MET cc_start: 0.8553 (mmp) cc_final: 0.8215 (mmp) REVERT: A 526 TRP cc_start: 0.8004 (m-10) cc_final: 0.7758 (m-10) REVERT: A 644 MET cc_start: 0.7925 (mmm) cc_final: 0.6369 (tmm) REVERT: A 688 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7835 (mm-30) REVERT: B 42 TRP cc_start: 0.8295 (m100) cc_final: 0.7757 (m100) REVERT: B 165 MET cc_start: 0.7421 (tmm) cc_final: 0.7206 (tmm) REVERT: B 176 MET cc_start: 0.8311 (tpp) cc_final: 0.8066 (tpp) REVERT: B 327 SER cc_start: 0.9015 (m) cc_final: 0.8717 (t) REVERT: B 344 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8069 (ttm110) REVERT: B 361 TYR cc_start: 0.8703 (t80) cc_final: 0.8049 (t80) REVERT: B 363 PRO cc_start: 0.9263 (Cg_exo) cc_final: 0.8949 (Cg_endo) REVERT: B 438 PHE cc_start: 0.8943 (m-10) cc_final: 0.8613 (m-10) REVERT: B 441 PHE cc_start: 0.7688 (m-80) cc_final: 0.7450 (m-80) REVERT: B 447 MET cc_start: 0.8995 (tpt) cc_final: 0.8555 (tpp) REVERT: B 452 PHE cc_start: 0.8835 (t80) cc_final: 0.8511 (t80) REVERT: B 479 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7621 (mp) REVERT: B 686 LEU cc_start: 0.9419 (mt) cc_final: 0.9210 (mt) outliers start: 41 outliers final: 32 residues processed: 304 average time/residue: 0.1871 time to fit residues: 86.6111 Evaluate side-chains 304 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 269 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 217 VAL 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 260 ASP 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 539 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 A residue 673 CYS Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 170 THR 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 565 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 691 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 15 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 49 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 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 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 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 = 0.3746 r_free = 0.3746 target = 0.133456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.116605 restraints weight = 18226.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.120037 restraints weight = 8201.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.122072 restraints weight = 4784.500| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9854 Z= 0.252 Angle : 0.800 16.973 13438 Z= 0.387 Chirality : 0.045 0.218 1548 Planarity : 0.005 0.052 1666 Dihedral : 5.557 57.840 1320 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 21.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.83 % Allowed : 32.82 % Favored : 63.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.25), residues: 1192 helix: 0.44 (0.18), residues: 824 sheet: -3.71 (1.04), residues: 24 loop : -2.36 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 625 HIS 0.004 0.001 HIS B 608 PHE 0.029 0.002 PHE A 396 TYR 0.067 0.002 TYR B 577 ARG 0.006 0.001 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3222.49 seconds wall clock time: 58 minutes 3.80 seconds (3483.80 seconds total)