Starting phenix.real_space_refine on Fri Feb 14 02:10:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jpf_6822/02_2025/6jpf_6822.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jpf_6822/02_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_6822/02_2025/6jpf_6822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jpf_6822/02_2025/6jpf_6822.map" model { file = "/net/cci-nas-00/data/ceres_data/6jpf_6822/02_2025/6jpf_6822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jpf_6822/02_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 8.74, per 1000 atoms: 0.91 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: 2.74 Conformation dependent library (CDL) restraints added in 1.2 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: 0.93 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: 2.92 Time building geometry restraints manager: 3.06 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.270 Find NCS groups from input model: 0.210 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.780 ------------------------------------------------------------------------------- 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 : 1.107 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: 0.1933 time to fit residues: 115.5578 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 : 1.096 ------------------------------------------------------------------------------- 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 = 30)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.104322 restraints weight = 18686.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.107585 restraints weight = 8246.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.109605 restraints weight = 4830.518| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 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 : 1.037 Fit side-chains REVERT: A 17 THR cc_start: 0.9302 (m) cc_final: 0.8612 (t) REVERT: A 30 LEU cc_start: 0.8877 (mt) cc_final: 0.8545 (pp) REVERT: A 36 ARG cc_start: 0.8999 (mtp180) cc_final: 0.8612 (ttm-80) REVERT: A 72 PHE cc_start: 0.6770 (t80) cc_final: 0.6555 (t80) REVERT: A 115 LEU cc_start: 0.9341 (tt) cc_final: 0.9038 (tt) REVERT: A 176 MET cc_start: 0.8371 (tpp) cc_final: 0.7984 (tpp) REVERT: A 201 GLN cc_start: 0.8649 (mt0) cc_final: 0.8189 (mp10) REVERT: A 208 ASN cc_start: 0.8230 (m-40) cc_final: 0.7933 (m-40) REVERT: A 226 LEU cc_start: 0.9277 (mt) cc_final: 0.8874 (mt) REVERT: A 247 ASP cc_start: 0.7616 (t70) cc_final: 0.7180 (t0) REVERT: A 257 ASN cc_start: 0.9098 (p0) cc_final: 0.8801 (m-40) REVERT: A 260 ASP cc_start: 0.8547 (m-30) cc_final: 0.8322 (t70) REVERT: A 360 ILE cc_start: 0.9082 (pt) cc_final: 0.8863 (pt) REVERT: A 361 TYR cc_start: 0.8544 (t80) cc_final: 0.7727 (t80) REVERT: A 363 PRO cc_start: 0.9366 (Cg_exo) cc_final: 0.8780 (Cg_endo) REVERT: A 376 ARG cc_start: 0.8339 (ttm110) cc_final: 0.8116 (mtm-85) REVERT: A 438 PHE cc_start: 0.8803 (m-10) cc_final: 0.8476 (m-10) REVERT: A 441 PHE cc_start: 0.7931 (m-80) cc_final: 0.7618 (m-80) REVERT: A 460 PHE cc_start: 0.8316 (t80) cc_final: 0.8100 (t80) REVERT: A 465 SER cc_start: 0.9278 (t) cc_final: 0.8978 (m) REVERT: A 479 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7563 (mp) REVERT: A 524 ASP cc_start: 0.9049 (t0) cc_final: 0.8796 (t70) REVERT: A 688 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8193 (mm-30) REVERT: B 30 LEU cc_start: 0.8879 (mt) cc_final: 0.8561 (pp) REVERT: B 36 ARG cc_start: 0.8607 (mmm160) cc_final: 0.8366 (mmm160) REVERT: B 94 ASP cc_start: 0.8058 (p0) cc_final: 0.7664 (p0) REVERT: B 115 LEU cc_start: 0.9339 (tt) cc_final: 0.8863 (tt) REVERT: B 208 ASN cc_start: 0.8304 (m-40) cc_final: 0.7981 (m-40) REVERT: B 226 LEU cc_start: 0.9227 (mt) cc_final: 0.8883 (mt) REVERT: B 247 ASP cc_start: 0.7599 (t70) cc_final: 0.7298 (t0) REVERT: B 257 ASN cc_start: 0.8464 (m-40) cc_final: 0.8078 (p0) REVERT: B 260 ASP cc_start: 0.8538 (m-30) cc_final: 0.8139 (t0) REVERT: B 344 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8183 (ttm110) REVERT: B 360 ILE cc_start: 0.9062 (pt) cc_final: 0.8801 (pt) REVERT: B 361 TYR cc_start: 0.8601 (t80) cc_final: 0.8339 (t80) REVERT: B 376 ARG cc_start: 0.8257 (ttm110) cc_final: 0.8031 (mtm-85) REVERT: B 430 LEU cc_start: 0.8060 (tp) cc_final: 0.7785 (tt) REVERT: B 438 PHE cc_start: 0.8957 (m-10) cc_final: 0.8620 (m-10) REVERT: B 441 PHE cc_start: 0.8047 (m-80) cc_final: 0.7709 (m-80) REVERT: B 479 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7395 (mp) REVERT: B 522 MET cc_start: 0.8662 (mmm) cc_final: 0.7891 (mmp) REVERT: B 565 ILE cc_start: 0.9164 (tp) cc_final: 0.8883 (tp) REVERT: B 633 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8621 (tp) REVERT: B 644 MET cc_start: 0.7427 (mtp) cc_final: 0.7147 (tmm) REVERT: B 686 LEU cc_start: 0.9477 (mt) cc_final: 0.9230 (mt) outliers start: 58 outliers final: 27 residues processed: 376 average time/residue: 0.1796 time to fit residues: 99.0498 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 : 1.088 ------------------------------------------------------------------------------- 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: 0.8980 chunk 11 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3589 r_free = 0.3589 target = 0.122004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.104111 restraints weight = 18706.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.107417 restraints weight = 8460.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.109491 restraints weight = 5032.843| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9854 Z= 0.314 Angle : 0.723 9.019 13438 Z= 0.370 Chirality : 0.045 0.166 1548 Planarity : 0.005 0.059 1666 Dihedral : 6.508 55.141 1332 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 6.31 % Allowed : 21.64 % Favored : 72.05 % 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: -1.65 (0.24), residues: 1192 helix: -0.33 (0.17), residues: 856 sheet: -3.87 (0.89), residues: 24 loop : -2.80 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 625 HIS 0.004 0.001 HIS A 608 PHE 0.019 0.002 PHE B 598 TYR 0.017 0.002 TYR A 102 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 370 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 309 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 PHE cc_start: 0.8843 (m-80) cc_final: 0.8357 (m-80) REVERT: A 36 ARG cc_start: 0.8993 (mtp180) cc_final: 0.8683 (tpp80) REVERT: A 115 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9009 (tt) REVERT: A 176 MET cc_start: 0.8409 (tpp) cc_final: 0.7925 (tpp) REVERT: A 201 GLN cc_start: 0.8469 (mt0) cc_final: 0.8202 (mp10) REVERT: A 361 TYR cc_start: 0.8748 (t80) cc_final: 0.8083 (t80) REVERT: A 363 PRO cc_start: 0.9350 (Cg_exo) cc_final: 0.9003 (Cg_endo) REVERT: A 438 PHE cc_start: 0.8874 (m-10) cc_final: 0.8505 (m-10) REVERT: A 441 PHE cc_start: 0.7780 (m-80) cc_final: 0.7434 (m-80) REVERT: A 460 PHE cc_start: 0.8395 (t80) cc_final: 0.8165 (t80) REVERT: A 461 LEU cc_start: 0.9090 (tt) cc_final: 0.8887 (tp) REVERT: A 465 SER cc_start: 0.9297 (t) cc_final: 0.8974 (m) REVERT: A 479 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7673 (mp) REVERT: A 522 MET cc_start: 0.8680 (mmm) cc_final: 0.8251 (mmp) REVERT: A 524 ASP cc_start: 0.9005 (t0) cc_final: 0.8738 (t70) REVERT: A 688 GLU cc_start: 0.8549 (mm-30) cc_final: 0.7874 (mm-30) REVERT: B 21 PHE cc_start: 0.8772 (m-80) cc_final: 0.8391 (m-80) REVERT: B 102 TYR cc_start: 0.8637 (m-10) cc_final: 0.8422 (m-10) REVERT: B 115 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9064 (tt) REVERT: B 176 MET cc_start: 0.8331 (tpp) cc_final: 0.8000 (tpp) REVERT: B 201 GLN cc_start: 0.8498 (mt0) cc_final: 0.8235 (mp10) REVERT: B 226 LEU cc_start: 0.9194 (mt) cc_final: 0.8890 (mt) REVERT: B 247 ASP cc_start: 0.7301 (t70) cc_final: 0.6922 (t0) REVERT: B 344 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8141 (ttm110) REVERT: B 361 TYR cc_start: 0.8799 (t80) cc_final: 0.8073 (t80) REVERT: B 363 PRO cc_start: 0.9426 (Cg_exo) cc_final: 0.8980 (Cg_endo) REVERT: B 376 ARG cc_start: 0.8303 (ttm110) cc_final: 0.8062 (mtm-85) REVERT: B 430 LEU cc_start: 0.8046 (tp) cc_final: 0.7806 (tt) REVERT: B 438 PHE cc_start: 0.9000 (m-10) cc_final: 0.8628 (m-10) REVERT: B 441 PHE cc_start: 0.7909 (m-80) cc_final: 0.7547 (m-80) REVERT: B 447 MET cc_start: 0.9090 (tpt) cc_final: 0.8800 (tpp) REVERT: B 479 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7574 (mp) REVERT: B 522 MET cc_start: 0.8626 (mmm) cc_final: 0.7933 (mmp) REVERT: B 524 ASP cc_start: 0.9098 (t0) cc_final: 0.8797 (t70) REVERT: B 616 GLN cc_start: 0.8013 (mm-40) cc_final: 0.7725 (mm-40) REVERT: B 686 LEU cc_start: 0.9514 (mt) cc_final: 0.9302 (mt) outliers start: 61 outliers final: 36 residues processed: 336 average time/residue: 0.1625 time to fit residues: 82.3567 Evaluate side-chains 325 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 284 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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 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 391 ILE Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 613 VAL 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: 1.9990 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3603 r_free = 0.3603 target = 0.123093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.105203 restraints weight = 18410.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.108446 restraints weight = 8402.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.110536 restraints weight = 5029.167| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9854 Z= 0.281 Angle : 0.707 9.723 13438 Z= 0.358 Chirality : 0.044 0.173 1548 Planarity : 0.005 0.058 1666 Dihedral : 6.271 48.110 1328 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 6.21 % Allowed : 24.64 % Favored : 69.15 % 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: -1.32 (0.24), residues: 1192 helix: -0.11 (0.17), residues: 852 sheet: -3.96 (0.91), residues: 24 loop : -2.55 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 625 HIS 0.004 0.001 HIS A 608 PHE 0.021 0.002 PHE A 396 TYR 0.018 0.002 TYR A 102 ARG 0.005 0.001 ARG A 344 *********************** 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 367 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 307 time to evaluate : 1.065 Fit side-chains REVERT: A 21 PHE cc_start: 0.8785 (m-80) cc_final: 0.8081 (m-80) REVERT: A 30 LEU cc_start: 0.8804 (mt) cc_final: 0.8496 (pp) REVERT: A 36 ARG cc_start: 0.8974 (mtp180) cc_final: 0.8416 (ttm170) REVERT: A 72 PHE cc_start: 0.6590 (t80) cc_final: 0.6370 (t80) REVERT: A 75 TRP cc_start: 0.7883 (t60) cc_final: 0.6695 (t60) REVERT: A 76 MET cc_start: 0.8254 (tpp) cc_final: 0.7604 (tpp) REVERT: A 82 MET cc_start: 0.8588 (tpp) cc_final: 0.8151 (ttt) REVERT: A 115 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9123 (tt) REVERT: A 176 MET cc_start: 0.8367 (tpp) cc_final: 0.7955 (tpp) REVERT: A 201 GLN cc_start: 0.8437 (mt0) cc_final: 0.8225 (mp10) REVERT: A 356 GLU cc_start: 0.8414 (mp0) cc_final: 0.8187 (mp0) REVERT: A 361 TYR cc_start: 0.8750 (t80) cc_final: 0.8077 (t80) REVERT: A 363 PRO cc_start: 0.9294 (Cg_exo) cc_final: 0.8994 (Cg_endo) REVERT: A 438 PHE cc_start: 0.8886 (m-10) cc_final: 0.8493 (m-10) REVERT: A 441 PHE cc_start: 0.7725 (m-80) cc_final: 0.7433 (m-80) REVERT: A 452 PHE cc_start: 0.9054 (t80) cc_final: 0.8162 (t80) REVERT: A 465 SER cc_start: 0.9306 (t) cc_final: 0.8987 (m) REVERT: A 479 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7652 (mp) REVERT: A 522 MET cc_start: 0.8491 (mmm) cc_final: 0.7848 (mmp) REVERT: A 524 ASP cc_start: 0.9023 (t0) cc_final: 0.8747 (t70) REVERT: A 526 TRP cc_start: 0.8515 (m-10) cc_final: 0.8208 (m-10) REVERT: A 688 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7781 (mm-30) REVERT: B 14 ASN cc_start: 0.9075 (m-40) cc_final: 0.8860 (t0) REVERT: B 21 PHE cc_start: 0.8774 (m-80) cc_final: 0.8095 (m-80) REVERT: B 30 LEU cc_start: 0.8747 (mt) cc_final: 0.8488 (pp) REVERT: B 94 ASP cc_start: 0.7875 (p0) cc_final: 0.7632 (p0) REVERT: B 95 SER cc_start: 0.9346 (p) cc_final: 0.9105 (p) REVERT: B 102 TYR cc_start: 0.8701 (m-10) cc_final: 0.8461 (m-10) REVERT: B 115 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9073 (tt) REVERT: B 176 MET cc_start: 0.8331 (tpp) cc_final: 0.7945 (tpp) REVERT: B 247 ASP cc_start: 0.7162 (t70) cc_final: 0.6812 (t0) REVERT: B 336 VAL cc_start: 0.8915 (OUTLIER) cc_final: 0.8708 (p) REVERT: B 344 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8100 (ttm110) REVERT: B 361 TYR cc_start: 0.8781 (t80) cc_final: 0.8101 (t80) REVERT: B 363 PRO cc_start: 0.9400 (Cg_exo) cc_final: 0.8976 (Cg_endo) REVERT: B 430 LEU cc_start: 0.8123 (tp) cc_final: 0.7908 (tt) REVERT: B 441 PHE cc_start: 0.7865 (m-80) cc_final: 0.7613 (m-80) REVERT: B 447 MET cc_start: 0.9095 (tpt) cc_final: 0.8814 (tpp) REVERT: B 522 MET cc_start: 0.8601 (mmm) cc_final: 0.7470 (mmp) REVERT: B 524 ASP cc_start: 0.9113 (t0) cc_final: 0.8778 (t70) REVERT: B 526 TRP cc_start: 0.8533 (m-10) cc_final: 0.8126 (m-10) REVERT: B 659 LEU cc_start: 0.8177 (mt) cc_final: 0.7867 (mt) REVERT: B 686 LEU cc_start: 0.9521 (mt) cc_final: 0.9275 (mt) outliers start: 60 outliers final: 44 residues processed: 337 average time/residue: 0.1634 time to fit residues: 83.6346 Evaluate side-chains 332 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 283 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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 234 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 390 PHE 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 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 A residue 714 ILE 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 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 259 LEU 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 482 VAL Chi-restraints excluded: chain B residue 510 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 80 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 91 optimal weight: 0.0980 chunk 99 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 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 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 616 GLN ** 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 = 0.3664 r_free = 0.3664 target = 0.127174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.109610 restraints weight = 18106.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.112919 restraints weight = 8244.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.115073 restraints weight = 4902.318| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9854 Z= 0.229 Angle : 0.700 10.052 13438 Z= 0.353 Chirality : 0.044 0.174 1548 Planarity : 0.005 0.055 1666 Dihedral : 6.237 59.169 1328 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 5.28 % Allowed : 26.19 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.93 (0.25), residues: 1192 helix: 0.17 (0.18), residues: 826 sheet: -4.03 (0.93), residues: 24 loop : -2.16 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 75 HIS 0.006 0.001 HIS B 608 PHE 0.019 0.002 PHE B 669 TYR 0.024 0.002 TYR A 102 ARG 0.003 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 369 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 318 time to evaluate : 1.092 Fit side-chains REVERT: A 21 PHE cc_start: 0.8681 (m-80) cc_final: 0.8095 (m-80) REVERT: A 30 LEU cc_start: 0.8827 (mt) cc_final: 0.8563 (pp) REVERT: A 75 TRP cc_start: 0.7815 (t60) cc_final: 0.7310 (t60) REVERT: A 76 MET cc_start: 0.8258 (tpp) cc_final: 0.7710 (tpp) REVERT: A 82 MET cc_start: 0.8501 (tpp) cc_final: 0.8125 (ttt) REVERT: A 115 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.8975 (tt) REVERT: A 247 ASP cc_start: 0.7559 (t70) cc_final: 0.7050 (t0) REVERT: A 361 TYR cc_start: 0.8590 (t80) cc_final: 0.7981 (t80) REVERT: A 363 PRO cc_start: 0.9314 (Cg_exo) cc_final: 0.8956 (Cg_endo) REVERT: A 438 PHE cc_start: 0.8833 (m-10) cc_final: 0.8462 (m-10) REVERT: A 441 PHE cc_start: 0.7703 (m-80) cc_final: 0.7365 (m-80) REVERT: A 452 PHE cc_start: 0.8996 (t80) cc_final: 0.8617 (t80) REVERT: A 465 SER cc_start: 0.9336 (t) cc_final: 0.8941 (m) REVERT: A 479 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7629 (mp) REVERT: A 510 ILE cc_start: 0.7316 (OUTLIER) cc_final: 0.7044 (mt) REVERT: A 522 MET cc_start: 0.8492 (mmm) cc_final: 0.7649 (mmp) REVERT: A 524 ASP cc_start: 0.9085 (t0) cc_final: 0.8675 (t70) REVERT: A 526 TRP cc_start: 0.8400 (m-10) cc_final: 0.8094 (m-10) REVERT: A 644 MET cc_start: 0.7620 (mmm) cc_final: 0.6651 (tmm) REVERT: A 688 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7726 (mm-30) REVERT: B 21 PHE cc_start: 0.8664 (m-80) cc_final: 0.7950 (m-80) REVERT: B 30 LEU cc_start: 0.8738 (mt) cc_final: 0.8521 (pp) REVERT: B 102 TYR cc_start: 0.8618 (m-10) cc_final: 0.8408 (m-10) REVERT: B 115 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8955 (tt) REVERT: B 176 MET cc_start: 0.8333 (tpp) cc_final: 0.8017 (tpp) REVERT: B 204 VAL cc_start: 0.9027 (p) cc_final: 0.8513 (p) REVERT: B 247 ASP cc_start: 0.7036 (t70) cc_final: 0.6669 (t0) REVERT: B 326 VAL cc_start: 0.9102 (t) cc_final: 0.8801 (p) REVERT: B 337 CYS cc_start: 0.8519 (t) cc_final: 0.8165 (t) REVERT: B 344 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8079 (ttm110) REVERT: B 361 TYR cc_start: 0.8659 (t80) cc_final: 0.8002 (t80) REVERT: B 363 PRO cc_start: 0.9333 (Cg_exo) cc_final: 0.8963 (Cg_endo) REVERT: B 430 LEU cc_start: 0.8271 (tp) cc_final: 0.8063 (tt) REVERT: B 438 PHE cc_start: 0.9001 (m-10) cc_final: 0.8649 (m-10) REVERT: B 441 PHE cc_start: 0.7784 (m-80) cc_final: 0.7549 (m-80) REVERT: B 447 MET cc_start: 0.9127 (tpt) cc_final: 0.8820 (tpp) REVERT: B 460 PHE cc_start: 0.8432 (t80) cc_final: 0.8231 (t80) REVERT: B 479 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7555 (mp) REVERT: B 522 MET cc_start: 0.8536 (mmm) cc_final: 0.7487 (mmp) REVERT: B 524 ASP cc_start: 0.9120 (t0) cc_final: 0.8740 (t70) REVERT: B 526 TRP cc_start: 0.8493 (m-10) cc_final: 0.8091 (m-10) REVERT: B 644 MET cc_start: 0.7583 (mmm) cc_final: 0.6727 (tmm) REVERT: B 686 LEU cc_start: 0.9496 (mt) cc_final: 0.9253 (mt) outliers start: 51 outliers final: 36 residues processed: 344 average time/residue: 0.1736 time to fit residues: 89.3845 Evaluate side-chains 325 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 283 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 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 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 167 TYR Chi-restraints excluded: chain B residue 170 THR 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 120 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 0.1980 chunk 61 optimal weight: 10.0000 chunk 38 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.129042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.112099 restraints weight = 18191.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.115417 restraints weight = 8103.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.117525 restraints weight = 4719.877| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9854 Z= 0.233 Angle : 0.717 10.577 13438 Z= 0.356 Chirality : 0.044 0.173 1548 Planarity : 0.005 0.055 1666 Dihedral : 5.795 45.423 1324 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.66 % Allowed : 27.43 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.79 (0.25), residues: 1192 helix: 0.27 (0.18), residues: 820 sheet: -3.87 (0.96), residues: 24 loop : -2.05 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 625 HIS 0.005 0.001 HIS B 608 PHE 0.024 0.002 PHE B 169 TYR 0.034 0.002 TYR A 102 ARG 0.003 0.001 ARG A 100 *********************** 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 347 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 302 time to evaluate : 1.002 Fit side-chains REVERT: A 30 LEU cc_start: 0.8826 (mt) cc_final: 0.8575 (pp) REVERT: A 75 TRP cc_start: 0.7836 (t60) cc_final: 0.7287 (t60) REVERT: A 76 MET cc_start: 0.8218 (tpp) cc_final: 0.7664 (tpp) REVERT: A 115 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9064 (tt) REVERT: A 176 MET cc_start: 0.8310 (tpp) cc_final: 0.8059 (tpp) REVERT: A 361 TYR cc_start: 0.8661 (t80) cc_final: 0.8089 (t80) REVERT: A 363 PRO cc_start: 0.9291 (Cg_exo) cc_final: 0.8910 (Cg_endo) REVERT: A 438 PHE cc_start: 0.8834 (m-10) cc_final: 0.8458 (m-10) REVERT: A 441 PHE cc_start: 0.7589 (m-80) cc_final: 0.7322 (m-80) REVERT: A 465 SER cc_start: 0.9296 (t) cc_final: 0.8993 (m) REVERT: A 479 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7696 (mp) REVERT: A 524 ASP cc_start: 0.9065 (t0) cc_final: 0.8628 (t70) REVERT: A 584 TYR cc_start: 0.8549 (m-10) cc_final: 0.8270 (m-10) REVERT: A 644 MET cc_start: 0.7705 (mmm) cc_final: 0.6377 (tmm) REVERT: A 688 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7710 (mm-30) REVERT: B 102 TYR cc_start: 0.8619 (m-10) cc_final: 0.8379 (m-10) REVERT: B 115 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9128 (tt) REVERT: B 344 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8049 (ttm110) REVERT: B 361 TYR cc_start: 0.8615 (t80) cc_final: 0.7960 (t80) REVERT: B 363 PRO cc_start: 0.9308 (Cg_exo) cc_final: 0.8931 (Cg_endo) REVERT: B 430 LEU cc_start: 0.8346 (tp) cc_final: 0.8113 (tt) REVERT: B 438 PHE cc_start: 0.8980 (m-10) cc_final: 0.8609 (m-10) REVERT: B 441 PHE cc_start: 0.7749 (m-80) cc_final: 0.7497 (m-80) REVERT: B 447 MET cc_start: 0.8998 (tpt) cc_final: 0.8581 (tpp) REVERT: B 460 PHE cc_start: 0.8435 (t80) cc_final: 0.8173 (t80) REVERT: B 479 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7602 (mp) REVERT: B 522 MET cc_start: 0.8538 (mmm) cc_final: 0.7914 (mmp) REVERT: B 524 ASP cc_start: 0.9144 (t0) cc_final: 0.8823 (t70) REVERT: B 526 TRP cc_start: 0.8419 (m-10) cc_final: 0.8195 (m-10) REVERT: B 644 MET cc_start: 0.7493 (mmm) cc_final: 0.6320 (tmm) REVERT: B 686 LEU cc_start: 0.9470 (mt) cc_final: 0.9260 (mt) outliers start: 45 outliers final: 35 residues processed: 322 average time/residue: 0.1640 time to fit residues: 79.2018 Evaluate side-chains 317 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 277 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain 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 167 TYR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 91 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3701 r_free = 0.3701 target = 0.129946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.112586 restraints weight = 18452.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.115961 restraints weight = 8339.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.118116 restraints weight = 4900.167| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9854 Z= 0.234 Angle : 0.723 11.173 13438 Z= 0.356 Chirality : 0.044 0.176 1548 Planarity : 0.005 0.051 1666 Dihedral : 5.656 51.594 1322 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 5.18 % Allowed : 28.78 % Favored : 66.05 % 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: 0.37 (0.18), residues: 814 sheet: -3.88 (0.96), residues: 24 loop : -2.12 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 625 HIS 0.004 0.001 HIS B 608 PHE 0.015 0.001 PHE B 669 TYR 0.039 0.002 TYR B 577 ARG 0.004 0.000 ARG B 468 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 296 time to evaluate : 1.019 Fit side-chains REVERT: A 30 LEU cc_start: 0.8857 (mt) cc_final: 0.8629 (pp) REVERT: A 115 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9086 (tt) REVERT: A 176 MET cc_start: 0.8324 (tpp) cc_final: 0.8071 (tpp) REVERT: A 247 ASP cc_start: 0.7452 (t70) cc_final: 0.6949 (t0) REVERT: A 361 TYR cc_start: 0.8635 (t80) cc_final: 0.8025 (t80) REVERT: A 363 PRO cc_start: 0.9285 (Cg_exo) cc_final: 0.8900 (Cg_endo) REVERT: A 441 PHE cc_start: 0.7565 (m-80) cc_final: 0.7260 (m-80) REVERT: A 458 VAL cc_start: 0.8768 (OUTLIER) cc_final: 0.8556 (p) REVERT: A 460 PHE cc_start: 0.8427 (t80) cc_final: 0.8191 (t80) REVERT: A 465 SER cc_start: 0.9261 (t) cc_final: 0.9002 (m) REVERT: A 479 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7655 (mp) REVERT: A 522 MET cc_start: 0.8935 (mmp) cc_final: 0.8565 (mmp) REVERT: A 524 ASP cc_start: 0.9053 (t0) cc_final: 0.8718 (t70) REVERT: A 526 TRP cc_start: 0.8462 (m-10) cc_final: 0.8049 (m-10) REVERT: A 644 MET cc_start: 0.7630 (mmm) cc_final: 0.6290 (tmm) REVERT: A 688 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7767 (mm-30) REVERT: B 21 PHE cc_start: 0.8585 (m-80) cc_final: 0.7809 (m-80) REVERT: B 102 TYR cc_start: 0.8569 (m-10) cc_final: 0.8330 (m-10) REVERT: B 115 LEU cc_start: 0.9376 (tt) cc_final: 0.9122 (tt) REVERT: B 344 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.7942 (ttm110) REVERT: B 361 TYR cc_start: 0.8588 (t80) cc_final: 0.7977 (t80) REVERT: B 363 PRO cc_start: 0.9259 (Cg_exo) cc_final: 0.8911 (Cg_endo) REVERT: B 430 LEU cc_start: 0.8310 (tp) cc_final: 0.8085 (tt) REVERT: B 438 PHE cc_start: 0.8965 (m-10) cc_final: 0.8593 (m-10) REVERT: B 441 PHE cc_start: 0.7760 (m-80) cc_final: 0.7515 (m-80) REVERT: B 447 MET cc_start: 0.8965 (tpt) cc_final: 0.8645 (tpp) REVERT: B 460 PHE cc_start: 0.8369 (t80) cc_final: 0.8145 (t80) REVERT: B 465 SER cc_start: 0.9299 (t) cc_final: 0.8994 (m) REVERT: B 479 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7587 (mp) REVERT: B 522 MET cc_start: 0.8653 (mmm) cc_final: 0.7893 (mmp) REVERT: B 524 ASP cc_start: 0.9026 (t0) cc_final: 0.8770 (t70) REVERT: B 526 TRP cc_start: 0.8329 (m-10) cc_final: 0.8113 (m-10) REVERT: B 577 TYR cc_start: 0.7374 (m-80) cc_final: 0.7011 (m-80) REVERT: B 644 MET cc_start: 0.7842 (mmm) cc_final: 0.6246 (tmm) REVERT: B 686 LEU cc_start: 0.9468 (mt) cc_final: 0.9229 (mt) outliers start: 50 outliers final: 36 residues processed: 319 average time/residue: 0.1627 time to fit residues: 78.6069 Evaluate side-chains 316 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 275 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 260 ASP 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 458 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 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 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 391 ILE Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 673 CYS Chi-restraints excluded: chain B residue 678 GLU Chi-restraints excluded: chain B residue 691 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 60 optimal weight: 0.1980 chunk 15 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 104 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 ** B 14 ASN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.132386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.115186 restraints weight = 18479.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118600 restraints weight = 8320.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.120800 restraints weight = 4848.603| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9854 Z= 0.219 Angle : 0.740 12.788 13438 Z= 0.360 Chirality : 0.044 0.301 1548 Planarity : 0.005 0.052 1666 Dihedral : 5.625 58.058 1322 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 5.18 % Allowed : 29.19 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.65 (0.25), residues: 1192 helix: 0.44 (0.18), residues: 818 sheet: -3.81 (0.99), residues: 24 loop : -2.20 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 625 HIS 0.004 0.001 HIS B 608 PHE 0.022 0.001 PHE A 72 TYR 0.032 0.002 TYR B 577 ARG 0.004 0.000 ARG B 683 *********************** 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 348 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 298 time to evaluate : 1.054 Fit side-chains REVERT: A 42 TRP cc_start: 0.8301 (m100) cc_final: 0.7743 (m100) REVERT: A 115 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9075 (tt) REVERT: A 176 MET cc_start: 0.8331 (tpp) cc_final: 0.7730 (tpp) REVERT: A 247 ASP cc_start: 0.7444 (t70) cc_final: 0.6944 (t0) REVERT: A 361 TYR cc_start: 0.8589 (t80) cc_final: 0.7971 (t80) REVERT: A 363 PRO cc_start: 0.9286 (Cg_exo) cc_final: 0.8768 (Cg_endo) REVERT: A 441 PHE cc_start: 0.7532 (m-80) cc_final: 0.7220 (m-80) REVERT: A 452 PHE cc_start: 0.8598 (t80) cc_final: 0.8307 (t80) REVERT: A 460 PHE cc_start: 0.8431 (t80) cc_final: 0.8208 (t80) REVERT: A 465 SER cc_start: 0.9238 (t) cc_final: 0.9003 (m) REVERT: A 479 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7684 (mp) REVERT: A 524 ASP cc_start: 0.9009 (t0) cc_final: 0.8809 (t70) REVERT: A 526 TRP cc_start: 0.8342 (m-10) cc_final: 0.7980 (m-10) REVERT: A 532 GLU cc_start: 0.6313 (tp30) cc_final: 0.6029 (tp30) REVERT: A 644 MET cc_start: 0.7798 (mmm) cc_final: 0.6373 (tmm) REVERT: A 688 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7633 (mm-30) REVERT: B 327 SER cc_start: 0.8995 (m) cc_final: 0.8663 (t) REVERT: B 344 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.7954 (ttm110) REVERT: B 361 TYR cc_start: 0.8620 (t80) cc_final: 0.7953 (t80) REVERT: B 363 PRO cc_start: 0.9244 (Cg_exo) cc_final: 0.8843 (Cg_endo) REVERT: B 430 LEU cc_start: 0.8295 (tp) cc_final: 0.8077 (tt) REVERT: B 438 PHE cc_start: 0.8949 (m-10) cc_final: 0.8580 (m-10) REVERT: B 441 PHE cc_start: 0.7754 (m-80) cc_final: 0.7485 (m-80) REVERT: B 447 MET cc_start: 0.8935 (tpt) cc_final: 0.8612 (tpp) REVERT: B 460 PHE cc_start: 0.8326 (t80) cc_final: 0.8100 (t80) REVERT: B 465 SER cc_start: 0.9304 (t) cc_final: 0.9001 (m) REVERT: B 479 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7645 (mp) REVERT: B 524 ASP cc_start: 0.9082 (t0) cc_final: 0.8745 (t70) REVERT: B 577 TYR cc_start: 0.7403 (m-80) cc_final: 0.7040 (m-80) REVERT: B 644 MET cc_start: 0.7898 (mmm) cc_final: 0.6360 (tmm) REVERT: B 686 LEU cc_start: 0.9474 (mt) cc_final: 0.9267 (mt) outliers start: 50 outliers final: 39 residues processed: 318 average time/residue: 0.1607 time to fit residues: 77.7521 Evaluate side-chains 324 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 281 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 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 390 PHE Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 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 667 ILE Chi-restraints excluded: chain B residue 673 CYS Chi-restraints excluded: chain B residue 678 GLU Chi-restraints excluded: chain B residue 691 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 85 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 21 optimal weight: 0.0980 chunk 73 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 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 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 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 = 0.3750 r_free = 0.3750 target = 0.133868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.117116 restraints weight = 18376.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.120557 restraints weight = 8219.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.122712 restraints weight = 4760.712| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9854 Z= 0.233 Angle : 0.767 12.308 13438 Z= 0.374 Chirality : 0.045 0.362 1548 Planarity : 0.005 0.050 1666 Dihedral : 5.708 58.665 1322 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 4.76 % Allowed : 30.75 % Favored : 64.49 % 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: -0.56 (0.25), residues: 1192 helix: 0.52 (0.18), residues: 820 sheet: -3.66 (1.02), residues: 24 loop : -2.20 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP B 625 HIS 0.004 0.001 HIS A 608 PHE 0.015 0.001 PHE A 669 TYR 0.030 0.002 TYR B 577 ARG 0.003 0.000 ARG B 683 *********************** 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 332 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 286 time to evaluate : 1.076 Fit side-chains REVERT: A 42 TRP cc_start: 0.8144 (m100) cc_final: 0.7623 (m100) REVERT: A 115 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9079 (tt) REVERT: A 176 MET cc_start: 0.8305 (tpp) cc_final: 0.8040 (tpp) REVERT: A 247 ASP cc_start: 0.7412 (t70) cc_final: 0.6915 (t0) REVERT: A 296 ILE cc_start: 0.8204 (mm) cc_final: 0.7788 (tp) REVERT: A 361 TYR cc_start: 0.8625 (t80) cc_final: 0.7970 (t80) REVERT: A 363 PRO cc_start: 0.9198 (Cg_exo) cc_final: 0.8710 (Cg_endo) REVERT: A 441 PHE cc_start: 0.7566 (m-80) cc_final: 0.7263 (m-80) REVERT: A 460 PHE cc_start: 0.8333 (t80) cc_final: 0.8077 (t80) REVERT: A 465 SER cc_start: 0.9208 (t) cc_final: 0.8964 (m) REVERT: A 688 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7541 (mm-30) REVERT: B 42 TRP cc_start: 0.8314 (m100) cc_final: 0.7797 (m100) REVERT: B 327 SER cc_start: 0.8996 (m) cc_final: 0.8664 (t) REVERT: B 344 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7902 (ttm110) REVERT: B 361 TYR cc_start: 0.8611 (t80) cc_final: 0.7993 (t80) REVERT: B 363 PRO cc_start: 0.9249 (Cg_exo) cc_final: 0.8873 (Cg_endo) REVERT: B 438 PHE cc_start: 0.8909 (m-10) cc_final: 0.8565 (m-10) REVERT: B 441 PHE cc_start: 0.7762 (m-80) cc_final: 0.7486 (m-80) REVERT: B 447 MET cc_start: 0.8886 (tpt) cc_final: 0.8593 (tpp) REVERT: B 458 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8501 (p) REVERT: B 460 PHE cc_start: 0.8310 (t80) cc_final: 0.8082 (t80) REVERT: B 465 SER cc_start: 0.9282 (t) cc_final: 0.9005 (m) REVERT: B 479 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7587 (mp) REVERT: B 524 ASP cc_start: 0.9099 (t0) cc_final: 0.8740 (t70) REVERT: B 577 TYR cc_start: 0.7370 (m-80) cc_final: 0.7116 (m-80) REVERT: B 644 MET cc_start: 0.7946 (mmm) cc_final: 0.6383 (tmm) REVERT: B 686 LEU cc_start: 0.9433 (mt) cc_final: 0.9192 (mt) outliers start: 46 outliers final: 36 residues processed: 306 average time/residue: 0.1565 time to fit residues: 72.9992 Evaluate side-chains 313 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 273 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 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 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 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 226 LEU 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 458 VAL 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 667 ILE Chi-restraints excluded: chain B residue 673 CYS Chi-restraints excluded: chain B residue 678 GLU Chi-restraints excluded: chain B residue 691 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 6 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 27 optimal weight: 0.0970 chunk 108 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 48 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 GLN 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 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.134501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.117672 restraints weight = 18527.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.121144 restraints weight = 8308.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.123176 restraints weight = 4823.997| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9854 Z= 0.236 Angle : 0.779 14.640 13438 Z= 0.377 Chirality : 0.046 0.357 1548 Planarity : 0.005 0.049 1666 Dihedral : 5.557 56.566 1322 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 20.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.35 % Allowed : 31.57 % Favored : 64.08 % 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: -0.57 (0.25), residues: 1192 helix: 0.51 (0.18), residues: 822 sheet: -3.69 (0.99), residues: 24 loop : -2.22 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 625 HIS 0.004 0.001 HIS A 608 PHE 0.022 0.001 PHE A 72 TYR 0.030 0.002 TYR A 577 ARG 0.003 0.000 ARG B 683 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 286 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 TRP cc_start: 0.8050 (m100) cc_final: 0.7556 (m100) REVERT: A 176 MET cc_start: 0.8439 (tpp) cc_final: 0.8164 (tpp) REVERT: A 247 ASP cc_start: 0.7341 (t70) cc_final: 0.6845 (t0) REVERT: A 361 TYR cc_start: 0.8507 (t80) cc_final: 0.7865 (t80) REVERT: A 363 PRO cc_start: 0.9181 (Cg_exo) cc_final: 0.8798 (Cg_endo) REVERT: A 441 PHE cc_start: 0.7516 (m-80) cc_final: 0.7220 (m-80) REVERT: A 460 PHE cc_start: 0.8423 (t80) cc_final: 0.8169 (t80) REVERT: A 465 SER cc_start: 0.9232 (t) cc_final: 0.8976 (m) REVERT: A 532 GLU cc_start: 0.6383 (tp30) cc_final: 0.6097 (tp30) REVERT: A 644 MET cc_start: 0.7837 (mmm) cc_final: 0.6430 (tmm) REVERT: A 688 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7547 (mm-30) REVERT: B 42 TRP cc_start: 0.8279 (m100) cc_final: 0.7922 (m100) REVERT: B 327 SER cc_start: 0.8980 (m) cc_final: 0.8720 (t) REVERT: B 344 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8043 (ttm110) REVERT: B 361 TYR cc_start: 0.8628 (t80) cc_final: 0.7981 (t80) REVERT: B 363 PRO cc_start: 0.9234 (Cg_exo) cc_final: 0.8737 (Cg_endo) REVERT: B 438 PHE cc_start: 0.8896 (m-10) cc_final: 0.8554 (m-10) REVERT: B 441 PHE cc_start: 0.7737 (m-80) cc_final: 0.7492 (m-80) REVERT: B 447 MET cc_start: 0.8883 (tpt) cc_final: 0.8635 (tpp) REVERT: B 452 PHE cc_start: 0.8803 (t80) cc_final: 0.8547 (t80) REVERT: B 458 VAL cc_start: 0.8745 (OUTLIER) cc_final: 0.8510 (p) REVERT: B 460 PHE cc_start: 0.8259 (t80) cc_final: 0.8033 (t80) REVERT: B 465 SER cc_start: 0.9256 (t) cc_final: 0.9007 (m) REVERT: B 479 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7581 (mp) REVERT: B 524 ASP cc_start: 0.9103 (t0) cc_final: 0.8499 (t70) REVERT: B 686 LEU cc_start: 0.9362 (mt) cc_final: 0.9137 (mt) REVERT: B 688 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6905 (mm-30) outliers start: 42 outliers final: 32 residues processed: 301 average time/residue: 0.1596 time to fit residues: 73.4535 Evaluate side-chains 311 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 276 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE 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 386 LEU Chi-restraints excluded: chain A residue 390 PHE 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 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 226 LEU 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 458 VAL 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 667 ILE Chi-restraints excluded: chain B residue 673 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 15 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 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 = 0.3758 r_free = 0.3758 target = 0.134625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.117543 restraints weight = 18342.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.121025 restraints weight = 8310.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.123205 restraints weight = 4861.780| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.5290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9854 Z= 0.242 Angle : 0.785 13.835 13438 Z= 0.380 Chirality : 0.045 0.357 1548 Planarity : 0.005 0.048 1666 Dihedral : 5.484 58.187 1322 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.93 % Allowed : 31.47 % 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: -0.53 (0.25), residues: 1192 helix: 0.57 (0.18), residues: 816 sheet: -3.74 (0.98), residues: 24 loop : -2.25 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 625 HIS 0.004 0.001 HIS B 608 PHE 0.045 0.002 PHE B 396 TYR 0.025 0.002 TYR B 577 ARG 0.003 0.000 ARG B 683 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3072.99 seconds wall clock time: 55 minutes 44.95 seconds (3344.95 seconds total)