Starting phenix.real_space_refine on Tue Aug 4 17:47:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k91_62184/08_2026/9k91_62184.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k91_62184/08_2026/9k91_62184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k91_62184/08_2026/9k91_62184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k91_62184/08_2026/9k91_62184.map" model { file = "/net/cci-nas-00/data/ceres_data/9k91_62184/08_2026/9k91_62184.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k91_62184/08_2026/9k91_62184.cif" } resolution = 3.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 38 5.16 5 C 3485 2.51 5 N 978 2.21 5 O 1014 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5517 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 714, 5515 Classifications: {'peptide': 714} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 676} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.47, per 1000 atoms: 0.27 Number of scatterers: 5517 At special positions: 0 Unit cell: (67.104, 64.308, 116.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 38 16.00 O 1014 8.00 N 978 7.00 C 3485 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 275.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" ND1 HIS A 651 " pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" ND1 HIS A 255 " 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1306 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 4 sheets defined 52.1% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 91 through 96 removed outlier: 3.629A pdb=" N LEU A 94 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 96 " --> pdb=" O GLN A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 123 removed outlier: 3.649A pdb=" N HIS A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 142 removed outlier: 3.506A pdb=" N LEU A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 156 removed outlier: 3.598A pdb=" N ILE A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 160 through 170 removed outlier: 3.576A pdb=" N THR A 170 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 200 Processing helix chain 'A' and resid 230 through 242 Processing helix chain 'A' and resid 257 through 265 Processing helix chain 'A' and resid 287 through 291 removed outlier: 3.744A pdb=" N SER A 290 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN A 291 " --> pdb=" O LYS A 288 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 287 through 291' Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 315 through 326 removed outlier: 3.857A pdb=" N TYR A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 335 Processing helix chain 'A' and resid 344 through 348 removed outlier: 3.958A pdb=" N ALA A 347 " --> pdb=" O GLY A 344 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 348 " --> pdb=" O PHE A 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 344 through 348' Processing helix chain 'A' and resid 359 through 371 Processing helix chain 'A' and resid 372 through 376 removed outlier: 4.982A pdb=" N GLY A 375 " --> pdb=" O GLY A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 403 Processing helix chain 'A' and resid 417 through 431 Processing helix chain 'A' and resid 486 through 492 removed outlier: 3.626A pdb=" N MET A 490 " --> pdb=" O ASP A 486 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N HIS A 492 " --> pdb=" O ASN A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 517 removed outlier: 3.935A pdb=" N LEU A 508 " --> pdb=" O PRO A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 523 removed outlier: 3.842A pdb=" N ARG A 522 " --> pdb=" O GLY A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 537 removed outlier: 3.693A pdb=" N LEU A 536 " --> pdb=" O THR A 532 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 537 " --> pdb=" O GLU A 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 532 through 537' Processing helix chain 'A' and resid 538 through 540 No H-bonds generated for 'chain 'A' and resid 538 through 540' Processing helix chain 'A' and resid 541 through 550 Processing helix chain 'A' and resid 555 through 566 removed outlier: 3.837A pdb=" N ARG A 561 " --> pdb=" O ARG A 557 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU A 562 " --> pdb=" O GLU A 558 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 564 " --> pdb=" O HIS A 560 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 595 Processing helix chain 'A' and resid 624 through 637 Processing helix chain 'A' and resid 653 through 660 removed outlier: 4.055A pdb=" N GLN A 657 " --> pdb=" O GLY A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 678 Processing helix chain 'A' and resid 711 through 722 removed outlier: 3.704A pdb=" N TYR A 715 " --> pdb=" O GLY A 711 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 718 " --> pdb=" O ASP A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 731 Processing helix chain 'A' and resid 740 through 744 Processing helix chain 'A' and resid 755 through 768 removed outlier: 3.598A pdb=" N LEU A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY A 768 " --> pdb=" O HIS A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 772 Processing helix chain 'A' and resid 783 through 800 removed outlier: 3.665A pdb=" N ILE A 787 " --> pdb=" O ASN A 783 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLU A 789 " --> pdb=" O THR A 785 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A 792 " --> pdb=" O SER A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 828 Processing helix chain 'A' and resid 831 through 835 removed outlier: 4.048A pdb=" N ARG A 835 " --> pdb=" O ARG A 832 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 131 removed outlier: 6.775A pdb=" N THR A 86 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N PHE A 131 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU A 88 " --> pdb=" O PHE A 131 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 89 " --> pdb=" O MET A 207 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 305 through 308 removed outlier: 7.622A pdb=" N ILE A 305 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N TYR A 272 " --> pdb=" O ILE A 305 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N VAL A 307 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N SER A 274 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU A 248 " --> pdb=" O LEU A 340 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ALA A 342 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL A 250 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 524 through 525 removed outlier: 6.224A pdb=" N THR A 481 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY A 482 " --> pdb=" O ALA A 602 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL A 604 " --> pdb=" O GLY A 482 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL A 484 " --> pdb=" O VAL A 604 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY A 601 " --> pdb=" O ILE A 774 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU A 644 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N SER A 738 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL A 646 " --> pdb=" O SER A 738 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 692 through 693 228 hydrogen bonds defined for protein. 648 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: 0.58 Time building geometry restraints manager: 0.73 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: 1865 1.34 - 1.46: 1232 1.46 - 1.58: 2501 1.58 - 1.70: 0 1.70 - 1.82: 57 Bond restraints: 5655 Sorted by residual: bond pdb=" C ARG A 211 " pdb=" N PRO A 212 " ideal model delta sigma weight residual 1.329 1.347 -0.018 1.18e-02 7.18e+03 2.30e+00 bond pdb=" CB ARG A 204 " pdb=" CG ARG A 204 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.07e+00 bond pdb=" C ARG A 606 " pdb=" O ARG A 606 " ideal model delta sigma weight residual 1.244 1.230 0.014 1.00e-02 1.00e+04 1.99e+00 bond pdb=" CA MET A 409 " pdb=" C MET A 409 " ideal model delta sigma weight residual 1.527 1.509 0.018 1.34e-02 5.57e+03 1.80e+00 bond pdb=" C PHE A 680 " pdb=" O PHE A 680 " ideal model delta sigma weight residual 1.241 1.229 0.012 9.80e-03 1.04e+04 1.48e+00 ... (remaining 5650 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 7423 2.02 - 4.05: 219 4.05 - 6.07: 43 6.07 - 8.09: 4 8.09 - 10.11: 5 Bond angle restraints: 7694 Sorted by residual: angle pdb=" N TYR A 782 " pdb=" CA TYR A 782 " pdb=" C TYR A 782 " ideal model delta sigma weight residual 108.30 116.57 -8.27 1.56e+00 4.11e-01 2.81e+01 angle pdb=" N LEU A 194 " pdb=" CA LEU A 194 " pdb=" C LEU A 194 " ideal model delta sigma weight residual 111.36 106.07 5.29 1.09e+00 8.42e-01 2.36e+01 angle pdb=" C ARG A 211 " pdb=" N PRO A 212 " pdb=" CA PRO A 212 " ideal model delta sigma weight residual 120.38 116.17 4.21 1.03e+00 9.43e-01 1.67e+01 angle pdb=" N MET A 682 " pdb=" CA MET A 682 " pdb=" C MET A 682 " ideal model delta sigma weight residual 111.30 105.87 5.43 1.36e+00 5.41e-01 1.59e+01 angle pdb=" CA ARG A 606 " pdb=" C ARG A 606 " pdb=" N PRO A 607 " ideal model delta sigma weight residual 120.81 117.39 3.42 8.60e-01 1.35e+00 1.58e+01 ... (remaining 7689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 2843 17.91 - 35.82: 358 35.82 - 53.73: 99 53.73 - 71.64: 22 71.64 - 89.55: 7 Dihedral angle restraints: 3329 sinusoidal: 1289 harmonic: 2040 Sorted by residual: dihedral pdb=" CA GLU A 432 " pdb=" C GLU A 432 " pdb=" N PRO A 433 " pdb=" CA PRO A 433 " ideal model delta harmonic sigma weight residual -180.00 -160.44 -19.56 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA GLN A 657 " pdb=" C GLN A 657 " pdb=" N HIS A 658 " pdb=" CA HIS A 658 " ideal model delta harmonic sigma weight residual 180.00 160.90 19.10 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA GLU A 383 " pdb=" C GLU A 383 " pdb=" N GLY A 384 " pdb=" CA GLY A 384 " ideal model delta harmonic sigma weight residual 180.00 -162.34 -17.66 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 3326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 662 0.052 - 0.104: 153 0.104 - 0.157: 25 0.157 - 0.209: 3 0.209 - 0.261: 1 Chirality restraints: 844 Sorted by residual: chirality pdb=" CA TYR A 782 " pdb=" N TYR A 782 " pdb=" C TYR A 782 " pdb=" CB TYR A 782 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CG LEU A 192 " pdb=" CB LEU A 192 " pdb=" CD1 LEU A 192 " pdb=" CD2 LEU A 192 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB THR A 763 " pdb=" CA THR A 763 " pdb=" OG1 THR A 763 " pdb=" CG2 THR A 763 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.16e-01 ... (remaining 841 not shown) Planarity restraints: 1011 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 705 " -0.014 2.00e-02 2.50e+03 1.44e-02 5.21e+00 pdb=" CG TRP A 705 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP A 705 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 705 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 705 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 705 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 705 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 705 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 705 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 705 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 108 " -0.036 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO A 109 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 109 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 109 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 284 " 0.036 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO A 285 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 285 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 285 " 0.031 5.00e-02 4.00e+02 ... (remaining 1008 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 33 2.47 - 3.08: 3834 3.08 - 3.69: 9216 3.69 - 4.29: 12694 4.29 - 4.90: 20395 Nonbonded interactions: 46172 Sorted by model distance: nonbonded pdb=" OD1 ASP A 253 " pdb="ZN ZN A 902 " model vdw 1.868 2.230 nonbonded pdb=" OD2 ASP A 253 " pdb="ZN ZN A 902 " model vdw 1.966 2.230 nonbonded pdb=" OD2 ASP A 346 " pdb="ZN ZN A 902 " model vdw 2.098 2.230 nonbonded pdb=" CG ASP A 253 " pdb="ZN ZN A 902 " model vdw 2.170 2.460 nonbonded pdb=" OD2 ASP A 649 " pdb="ZN ZN A 901 " model vdw 2.196 2.230 ... (remaining 46167 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.740 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.860 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 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 0.243 5657 Z= 0.227 Angle : 0.818 10.114 7694 Z= 0.465 Chirality : 0.047 0.261 844 Planarity : 0.006 0.055 1011 Dihedral : 17.415 89.549 2023 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.86 % Allowed : 30.57 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.30), residues: 710 helix: -0.44 (0.30), residues: 283 sheet: -1.07 (0.72), residues: 63 loop : -1.39 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 389 TYR 0.026 0.002 TYR A 237 PHE 0.018 0.001 PHE A 228 TRP 0.038 0.002 TRP A 705 HIS 0.007 0.001 HIS A 827 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.20 ( 5655) covalent geometry : angle 0.81812 / 0.47 ( 7694) hydrogen bonds : bond 0.18072 / 12.02 ( 228) hydrogen bonds : angle 7.11829 / 4.95 ( 648) metal coordination : bond 0.17255 / 9.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 135 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 GLN cc_start: 0.7672 (tp-100) cc_final: 0.7339 (tm-30) outliers start: 5 outliers final: 1 residues processed: 138 average time/residue: 0.0755 time to fit residues: 13.6706 Evaluate side-chains 127 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 755 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 ASN ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.198790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.151944 restraints weight = 9274.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.157642 restraints weight = 5422.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.161596 restraints weight = 3843.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.164251 restraints weight = 3062.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.165814 restraints weight = 2644.432| |-----------------------------------------------------------------------------| r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 5657 Z= 0.248 Angle : 0.725 9.309 7694 Z= 0.372 Chirality : 0.044 0.135 844 Planarity : 0.006 0.062 1011 Dihedral : 5.128 51.882 778 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 6.91 % Allowed : 24.18 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.32), residues: 710 helix: 0.29 (0.30), residues: 297 sheet: -1.50 (0.69), residues: 63 loop : -1.01 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 606 TYR 0.020 0.002 TYR A 278 PHE 0.016 0.002 PHE A 131 TRP 0.018 0.002 TRP A 309 HIS 0.012 0.002 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.25 ( 5655) covalent geometry : angle 0.72532 / 0.37 ( 7694) hydrogen bonds : bond 0.04124 / 2.72 ( 228) hydrogen bonds : angle 5.47678 / 3.75 ( 648) metal coordination : bond 0.00556 / 0.29 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 131 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.6885 (p90) REVERT: A 122 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8541 (mp0) REVERT: A 196 ASP cc_start: 0.8115 (m-30) cc_final: 0.7501 (m-30) REVERT: A 248 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8135 (tp) REVERT: A 333 GLU cc_start: 0.8417 (tt0) cc_final: 0.8108 (mt-10) REVERT: A 337 GLN cc_start: 0.8004 (tp-100) cc_final: 0.7780 (tm-30) REVERT: A 370 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8970 (mp) REVERT: A 822 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7843 (mm-30) outliers start: 40 outliers final: 21 residues processed: 155 average time/residue: 0.0620 time to fit residues: 13.1138 Evaluate side-chains 147 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 98 HIS Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 540 HIS Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 774 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 36 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 35 optimal weight: 0.0370 chunk 48 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 overall best weight: 2.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 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 = 0.4492 r_free = 0.4492 target = 0.202885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.155819 restraints weight = 9080.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.161584 restraints weight = 5236.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.165479 restraints weight = 3693.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.167992 restraints weight = 2941.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.169573 restraints weight = 2548.864| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5657 Z= 0.208 Angle : 0.685 9.931 7694 Z= 0.343 Chirality : 0.043 0.136 844 Planarity : 0.006 0.070 1011 Dihedral : 5.098 49.080 778 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 5.87 % Allowed : 26.94 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.32), residues: 710 helix: 0.43 (0.30), residues: 296 sheet: -1.80 (0.68), residues: 64 loop : -0.85 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 606 TYR 0.015 0.002 TYR A 386 PHE 0.019 0.002 PHE A 334 TRP 0.017 0.002 TRP A 309 HIS 0.010 0.002 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.21 ( 5655) covalent geometry : angle 0.68501 / 0.34 ( 7694) hydrogen bonds : bond 0.03937 / 2.59 ( 228) hydrogen bonds : angle 5.30326 / 3.66 ( 648) metal coordination : bond 0.00386 / 0.20 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.6686 (p90) REVERT: A 196 ASP cc_start: 0.8151 (m-30) cc_final: 0.7715 (m-30) REVERT: A 204 ARG cc_start: 0.8086 (tpp-160) cc_final: 0.7565 (tpp-160) REVERT: A 248 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8162 (tp) REVERT: A 333 GLU cc_start: 0.8267 (tt0) cc_final: 0.8026 (tt0) REVERT: A 370 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8923 (mp) outliers start: 34 outliers final: 22 residues processed: 147 average time/residue: 0.0580 time to fit residues: 11.7162 Evaluate side-chains 141 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 98 HIS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 292 TRP Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 540 HIS Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 774 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 32 optimal weight: 0.3980 chunk 55 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 58 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 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 = 0.4466 r_free = 0.4466 target = 0.200077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.152876 restraints weight = 9252.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.158559 restraints weight = 5371.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.162327 restraints weight = 3821.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.164862 restraints weight = 3073.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.166334 restraints weight = 2664.570| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 5657 Z= 0.238 Angle : 0.710 9.323 7694 Z= 0.360 Chirality : 0.044 0.146 844 Planarity : 0.005 0.047 1011 Dihedral : 5.332 51.152 778 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 7.94 % Allowed : 27.46 % Favored : 64.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.32), residues: 710 helix: 0.26 (0.30), residues: 296 sheet: -2.04 (0.68), residues: 65 loop : -0.83 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 606 TYR 0.022 0.002 TYR A 278 PHE 0.011 0.002 PHE A 273 TRP 0.012 0.002 TRP A 705 HIS 0.013 0.002 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.24 ( 5655) covalent geometry : angle 0.71037 / 0.36 ( 7694) hydrogen bonds : bond 0.03727 / 2.47 ( 228) hydrogen bonds : angle 5.32197 / 3.69 ( 648) metal coordination : bond 0.00281 / 0.14 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 121 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 97 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.6669 (p90) REVERT: A 196 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7500 (m-30) REVERT: A 204 ARG cc_start: 0.8108 (tpp-160) cc_final: 0.7486 (tpp-160) REVERT: A 248 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8226 (tp) REVERT: A 370 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8967 (mp) REVERT: A 822 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7938 (mm-30) outliers start: 46 outliers final: 32 residues processed: 147 average time/residue: 0.0488 time to fit residues: 10.3539 Evaluate side-chains 151 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 98 HIS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 292 TRP Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 540 HIS Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 774 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 43 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 49 optimal weight: 30.0000 chunk 64 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 40 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 702 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.198181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.151660 restraints weight = 9360.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.157260 restraints weight = 5380.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.161042 restraints weight = 3777.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.163504 restraints weight = 3006.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.164949 restraints weight = 2594.409| |-----------------------------------------------------------------------------| r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 5657 Z= 0.245 Angle : 0.724 10.156 7694 Z= 0.366 Chirality : 0.045 0.210 844 Planarity : 0.006 0.047 1011 Dihedral : 5.430 52.810 778 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 8.64 % Allowed : 28.32 % Favored : 63.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.32), residues: 710 helix: 0.21 (0.29), residues: 296 sheet: -2.08 (0.69), residues: 65 loop : -0.92 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 606 TYR 0.021 0.002 TYR A 386 PHE 0.011 0.002 PHE A 273 TRP 0.014 0.002 TRP A 705 HIS 0.012 0.002 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.25 ( 5655) covalent geometry : angle 0.72426 / 0.37 ( 7694) hydrogen bonds : bond 0.03725 / 2.46 ( 228) hydrogen bonds : angle 5.30618 / 3.69 ( 648) metal coordination : bond 0.00285 / 0.14 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 120 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 97 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.6626 (p90) REVERT: A 177 HIS cc_start: 0.6881 (t70) cc_final: 0.6409 (t70) REVERT: A 196 ASP cc_start: 0.8124 (m-30) cc_final: 0.7921 (m-30) REVERT: A 248 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8282 (tp) REVERT: A 337 GLN cc_start: 0.8101 (tm-30) cc_final: 0.7573 (tm-30) REVERT: A 369 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8501 (mm) REVERT: A 370 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8956 (mp) outliers start: 50 outliers final: 33 residues processed: 146 average time/residue: 0.0564 time to fit residues: 11.5731 Evaluate side-chains 155 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 98 HIS Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 292 TRP Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 540 HIS Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 774 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 22 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 634 GLN A 702 ASN ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.203626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.157613 restraints weight = 9116.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.163410 restraints weight = 5202.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.167386 restraints weight = 3619.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.169960 restraints weight = 2851.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.171482 restraints weight = 2451.967| |-----------------------------------------------------------------------------| r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 5657 Z= 0.137 Angle : 0.675 13.890 7694 Z= 0.330 Chirality : 0.043 0.214 844 Planarity : 0.005 0.045 1011 Dihedral : 5.058 48.345 778 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 6.22 % Allowed : 30.22 % Favored : 63.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.32), residues: 710 helix: 0.62 (0.31), residues: 296 sheet: -1.79 (0.64), residues: 73 loop : -0.78 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 606 TYR 0.017 0.002 TYR A 386 PHE 0.019 0.001 PHE A 228 TRP 0.016 0.002 TRP A 705 HIS 0.005 0.001 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 5655) covalent geometry : angle 0.67481 / 0.33 ( 7694) hydrogen bonds : bond 0.03320 / 2.24 ( 228) hydrogen bonds : angle 4.97353 / 3.46 ( 648) metal coordination : bond 0.00041 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.6704 (p90) REVERT: A 142 MET cc_start: 0.8220 (mmm) cc_final: 0.7897 (mmm) REVERT: A 177 HIS cc_start: 0.6751 (t70) cc_final: 0.6237 (t70) REVERT: A 196 ASP cc_start: 0.8152 (m-30) cc_final: 0.7665 (m-30) REVERT: A 204 ARG cc_start: 0.8033 (tpp-160) cc_final: 0.7392 (tpp-160) REVERT: A 337 GLN cc_start: 0.7938 (tm-30) cc_final: 0.7347 (tm-30) REVERT: A 356 MET cc_start: 0.6534 (OUTLIER) cc_final: 0.6324 (tpp) REVERT: A 370 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8896 (mp) REVERT: A 822 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7836 (mm-30) outliers start: 36 outliers final: 29 residues processed: 142 average time/residue: 0.0492 time to fit residues: 9.7293 Evaluate side-chains 151 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 98 HIS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 292 TRP Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 540 HIS Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 702 ASN Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 774 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 44 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 18 optimal weight: 0.0980 chunk 8 optimal weight: 7.9990 chunk 68 optimal weight: 0.0970 chunk 43 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 15 optimal weight: 0.2980 chunk 56 optimal weight: 0.3980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 634 GLN ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.207200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.160754 restraints weight = 9172.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.166735 restraints weight = 5271.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.170907 restraints weight = 3677.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.173617 restraints weight = 2897.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.175246 restraints weight = 2471.623| |-----------------------------------------------------------------------------| r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5657 Z= 0.118 Angle : 0.661 15.013 7694 Z= 0.321 Chirality : 0.043 0.213 844 Planarity : 0.005 0.047 1011 Dihedral : 4.708 39.944 778 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 5.35 % Allowed : 32.12 % Favored : 62.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.32), residues: 710 helix: 0.83 (0.31), residues: 296 sheet: -1.61 (0.71), residues: 64 loop : -0.83 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 529 TYR 0.021 0.002 TYR A 237 PHE 0.010 0.001 PHE A 699 TRP 0.017 0.001 TRP A 705 HIS 0.006 0.001 HIS A 827 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 5655) covalent geometry : angle 0.66125 / 0.32 ( 7694) hydrogen bonds : bond 0.03197 / 2.18 ( 228) hydrogen bonds : angle 4.81895 / 3.35 ( 648) metal coordination : bond 0.00013 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.6532 (p90) REVERT: A 142 MET cc_start: 0.8194 (mmm) cc_final: 0.7878 (mmm) REVERT: A 204 ARG cc_start: 0.8015 (tpp-160) cc_final: 0.7190 (tpp-160) REVERT: A 335 GLN cc_start: 0.9047 (pp30) cc_final: 0.8817 (tm-30) REVERT: A 337 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7281 (tm-30) REVERT: A 370 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8846 (mp) outliers start: 31 outliers final: 21 residues processed: 138 average time/residue: 0.0444 time to fit residues: 8.5448 Evaluate side-chains 143 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 98 HIS Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 149 TYR Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 292 TRP Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 540 HIS Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 774 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 26 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 56 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 37 optimal weight: 40.0000 chunk 51 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 GLN ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.207052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.159088 restraints weight = 9245.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.164792 restraints weight = 5430.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.168729 restraints weight = 3867.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.171292 restraints weight = 3101.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.172737 restraints weight = 2685.687| |-----------------------------------------------------------------------------| r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 5657 Z= 0.147 Angle : 0.674 12.527 7694 Z= 0.332 Chirality : 0.043 0.207 844 Planarity : 0.005 0.046 1011 Dihedral : 4.500 19.108 777 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 6.22 % Allowed : 31.26 % Favored : 62.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.32), residues: 710 helix: 0.83 (0.31), residues: 296 sheet: -1.45 (0.68), residues: 70 loop : -0.83 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 606 TYR 0.015 0.001 TYR A 386 PHE 0.010 0.001 PHE A 273 TRP 0.012 0.001 TRP A 705 HIS 0.007 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 5655) covalent geometry : angle 0.67450 / 0.33 ( 7694) hydrogen bonds : bond 0.03192 / 2.19 ( 228) hydrogen bonds : angle 4.88762 / 3.40 ( 648) metal coordination : bond 0.00154 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.6560 (p90) REVERT: A 142 MET cc_start: 0.8315 (mmm) cc_final: 0.8037 (mmm) REVERT: A 154 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7689 (mm-30) REVERT: A 177 HIS cc_start: 0.6749 (t70) cc_final: 0.6181 (t70) REVERT: A 196 ASP cc_start: 0.8122 (m-30) cc_final: 0.7662 (m-30) REVERT: A 204 ARG cc_start: 0.8004 (tpp-160) cc_final: 0.7169 (tpp-160) REVERT: A 335 GLN cc_start: 0.9071 (pp30) cc_final: 0.8795 (tm-30) REVERT: A 370 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8919 (mp) outliers start: 36 outliers final: 27 residues processed: 140 average time/residue: 0.0427 time to fit residues: 8.3648 Evaluate side-chains 149 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 98 HIS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 149 TYR Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 292 TRP Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 540 HIS Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 774 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 43 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 9 optimal weight: 8.9990 chunk 68 optimal weight: 0.0270 chunk 2 optimal weight: 0.3980 chunk 37 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 0.0070 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 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 = 0.4554 r_free = 0.4554 target = 0.210009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.163591 restraints weight = 9173.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.169806 restraints weight = 5212.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.174029 restraints weight = 3608.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.176824 restraints weight = 2832.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.178686 restraints weight = 2414.540| |-----------------------------------------------------------------------------| r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 5657 Z= 0.117 Angle : 0.696 16.288 7694 Z= 0.331 Chirality : 0.043 0.218 844 Planarity : 0.005 0.047 1011 Dihedral : 4.321 16.681 777 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 5.18 % Allowed : 31.43 % Favored : 63.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.32), residues: 710 helix: 0.94 (0.31), residues: 295 sheet: -1.38 (0.66), residues: 69 loop : -0.86 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 529 TYR 0.015 0.001 TYR A 386 PHE 0.021 0.001 PHE A 228 TRP 0.017 0.001 TRP A 705 HIS 0.004 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 5655) covalent geometry : angle 0.69642 / 0.33 ( 7694) hydrogen bonds : bond 0.03114 / 2.13 ( 228) hydrogen bonds : angle 4.72651 / 3.29 ( 648) metal coordination : bond 0.00051 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.6728 (p90) REVERT: A 122 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8561 (mp0) REVERT: A 142 MET cc_start: 0.8068 (mmm) cc_final: 0.7770 (mmm) REVERT: A 177 HIS cc_start: 0.6639 (t70) cc_final: 0.6076 (t70) REVERT: A 196 ASP cc_start: 0.8152 (m-30) cc_final: 0.7621 (m-30) REVERT: A 204 ARG cc_start: 0.7975 (tpp-160) cc_final: 0.7067 (tpp-160) REVERT: A 335 GLN cc_start: 0.9051 (pp30) cc_final: 0.8726 (tm-30) REVERT: A 370 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8813 (mp) REVERT: A 432 GLU cc_start: 0.7289 (mp0) cc_final: 0.6987 (mp0) REVERT: A 669 VAL cc_start: 0.9030 (t) cc_final: 0.8647 (p) outliers start: 30 outliers final: 20 residues processed: 140 average time/residue: 0.0517 time to fit residues: 10.0991 Evaluate side-chains 138 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 292 TRP Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 540 HIS Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 827 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 45 optimal weight: 0.9990 chunk 20 optimal weight: 0.0170 chunk 41 optimal weight: 10.0000 chunk 67 optimal weight: 0.2980 chunk 43 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 overall best weight: 0.6624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 GLN ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.209143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.163064 restraints weight = 9073.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.169151 restraints weight = 5215.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.173285 restraints weight = 3633.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.176055 restraints weight = 2864.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.177675 restraints weight = 2445.274| |-----------------------------------------------------------------------------| r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 5657 Z= 0.122 Angle : 0.688 15.163 7694 Z= 0.334 Chirality : 0.043 0.212 844 Planarity : 0.005 0.046 1011 Dihedral : 4.298 17.607 777 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.84 % Allowed : 32.30 % Favored : 62.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.32), residues: 710 helix: 0.93 (0.31), residues: 295 sheet: -1.28 (0.66), residues: 68 loop : -0.82 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 236 TYR 0.045 0.002 TYR A 237 PHE 0.010 0.001 PHE A 105 TRP 0.014 0.001 TRP A 705 HIS 0.004 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 5655) covalent geometry : angle 0.68849 / 0.33 ( 7694) hydrogen bonds : bond 0.03105 / 2.12 ( 228) hydrogen bonds : angle 4.71628 / 3.29 ( 648) metal coordination : bond 0.00049 / 0.03 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.6664 (p90) REVERT: A 122 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8528 (mp0) REVERT: A 142 MET cc_start: 0.8084 (mmm) cc_final: 0.7755 (mmm) REVERT: A 177 HIS cc_start: 0.6681 (t70) cc_final: 0.6147 (t70) REVERT: A 196 ASP cc_start: 0.8101 (m-30) cc_final: 0.7885 (m-30) REVERT: A 204 ARG cc_start: 0.8010 (tpp-160) cc_final: 0.7043 (tpp-160) REVERT: A 335 GLN cc_start: 0.9049 (pp30) cc_final: 0.8711 (tm-30) REVERT: A 370 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8818 (mp) REVERT: A 432 GLU cc_start: 0.7255 (mp0) cc_final: 0.6945 (mp0) outliers start: 28 outliers final: 22 residues processed: 133 average time/residue: 0.0548 time to fit residues: 10.1142 Evaluate side-chains 143 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 149 TYR Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 292 TRP Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 540 HIS Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 827 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 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 = 0.4515 r_free = 0.4515 target = 0.205624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.158456 restraints weight = 9262.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.164506 restraints weight = 5309.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.168556 restraints weight = 3720.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.171256 restraints weight = 2960.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.172792 restraints weight = 2549.312| |-----------------------------------------------------------------------------| r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 5657 Z= 0.161 Angle : 0.702 13.609 7694 Z= 0.344 Chirality : 0.044 0.203 844 Planarity : 0.005 0.044 1011 Dihedral : 4.417 17.992 777 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.01 % Allowed : 31.78 % Favored : 63.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.32), residues: 710 helix: 0.81 (0.31), residues: 295 sheet: -1.34 (0.64), residues: 70 loop : -0.76 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 832 TYR 0.038 0.002 TYR A 237 PHE 0.020 0.002 PHE A 334 TRP 0.014 0.001 TRP A 705 HIS 0.008 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 5655) covalent geometry : angle 0.70215 / 0.34 ( 7694) hydrogen bonds : bond 0.03194 / 2.16 ( 228) hydrogen bonds : angle 4.82676 / 3.38 ( 648) metal coordination : bond 0.00154 / 0.08 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 968.27 seconds wall clock time: 17 minutes 27.18 seconds (1047.18 seconds total)