Starting phenix.real_space_refine on Thu Jul 2 03:52:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7li9_23364/07_2026/7li9_23364.cif Found real_map, /net/cci-nas-00/data/ceres_data/7li9_23364/07_2026/7li9_23364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7li9_23364/07_2026/7li9_23364.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7li9_23364/07_2026/7li9_23364.cif" model { file = "/net/cci-nas-00/data/ceres_data/7li9_23364/07_2026/7li9_23364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7li9_23364/07_2026/7li9_23364.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7li9_23364/07_2026/7li9_23364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7li9_23364/07_2026/7li9_23364.map" } resolution = 3.9 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= 0.032 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 S 34 5.16 5 Cl 1 4.86 5 C 4090 2.51 5 N 966 2.21 5 O 1083 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6174 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4305 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 23, 'TRANS': 515} Chain: "B" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "C" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 829 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 100 Unusual residues: {' CL': 1, 'D10': 3, 'D12': 2, 'HP6': 2, 'LNK': 1, 'SRO': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Time building chain proxies: 1.61, per 1000 atoms: 0.26 Number of scatterers: 6174 At special positions: 0 Unit cell: (68.929, 74.5395, 122.63, 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) Cl 1 17.00 S 34 16.00 O 1083 8.00 N 966 7.00 C 4090 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 112 " distance=2.03 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=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG D 1 " - " ASN A 208 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 283.8 milliseconds 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1400 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 7 sheets defined 52.4% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 81 through 94 Processing helix chain 'A' and resid 99 through 113 removed outlier: 4.928A pdb=" N PHE A 105 " --> pdb=" O ASN A 101 " (cutoff:3.500A) Proline residue: A 106 - end of helix Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'A' and resid 129 through 144 Processing helix chain 'A' and resid 148 through 153 removed outlier: 3.657A pdb=" N TRP A 151 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 190 removed outlier: 4.148A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N THR A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ILE A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET A 180 " --> pdb=" O TYR A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 199 removed outlier: 3.567A pdb=" N SER A 199 " --> pdb=" O PRO A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 235 Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 252 through 268 removed outlier: 3.770A pdb=" N CYS A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 285 removed outlier: 3.676A pdb=" N TRP A 282 " --> pdb=" O GLY A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 301 removed outlier: 3.771A pdb=" N ILE A 290 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 316 through 320 removed outlier: 3.957A pdb=" N LYS A 319 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 320 " --> pdb=" O TRP A 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 316 through 320' Processing helix chain 'A' and resid 325 through 338 removed outlier: 3.738A pdb=" N GLY A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 349 removed outlier: 3.774A pdb=" N ALA A 346 " --> pdb=" O GLY A 342 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 347 " --> pdb=" O VAL A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 391 Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.734A pdb=" N VAL A 397 " --> pdb=" O VAL A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 415 removed outlier: 4.068A pdb=" N ALA A 411 " --> pdb=" O PHE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 451 removed outlier: 3.587A pdb=" N GLY A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 450 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 477 Processing helix chain 'A' and resid 478 through 482 Processing helix chain 'A' and resid 484 through 495 removed outlier: 3.632A pdb=" N VAL A 488 " --> pdb=" O GLY A 484 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 491 " --> pdb=" O TYR A 487 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 515 removed outlier: 4.036A pdb=" N LEU A 502 " --> pdb=" O GLY A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 529 Processing helix chain 'A' and resid 534 through 558 removed outlier: 3.514A pdb=" N ARG A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS A 540 " --> pdb=" O PHE A 536 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP A 541 " --> pdb=" O TRP A 537 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N SER A 545 " --> pdb=" O TRP A 541 " (cutoff:3.500A) Proline residue: A 546 - end of helix Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.841A pdb=" N ILE A 576 " --> pdb=" O TYR A 572 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 600 removed outlier: 3.551A pdb=" N LEU A 597 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE A 598 " --> pdb=" O ALA A 594 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE A 599 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR A 600 " --> pdb=" O ARG A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 613 removed outlier: 3.583A pdb=" N THR A 613 " --> pdb=" O ILE A 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 removed outlier: 4.092A pdb=" N TYR B 50 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER B 51 " --> pdb=" O PHE B 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 47 through 51' Processing sheet with id=AA1, first strand: chain 'A' and resid 564 through 565 Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 25 removed outlier: 3.689A pdb=" N SER B 44 " --> pdb=" O GLN B 22 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE B 39 " --> pdb=" O MET B 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'B' and resid 64 through 66 Processing sheet with id=AA5, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 78 removed outlier: 3.696A pdb=" N TYR C 73 " --> pdb=" O ASN C 77 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TRP C 59 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N TYR C 73 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU C 57 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN C 113 " --> pdb=" O ASN C 58 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 87 through 89 removed outlier: 3.522A pdb=" N SER C 96 " --> pdb=" O SER C 89 " (cutoff:3.500A) 268 hydrogen bonds defined for protein. 756 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: 0.88 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1817 1.34 - 1.46: 1646 1.46 - 1.58: 2835 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 6347 Sorted by residual: bond pdb=" CD1 SRO A 910 " pdb=" NE1 SRO A 910 " ideal model delta sigma weight residual 1.377 1.324 0.053 2.00e-02 2.50e+03 7.08e+00 bond pdb=" CD1 SRO A 909 " pdb=" NE1 SRO A 909 " ideal model delta sigma weight residual 1.377 1.324 0.053 2.00e-02 2.50e+03 7.01e+00 bond pdb=" CD2 SRO A 909 " pdb=" CE2 SRO A 909 " ideal model delta sigma weight residual 1.419 1.370 0.049 2.00e-02 2.50e+03 6.02e+00 bond pdb=" CD2 SRO A 910 " pdb=" CE2 SRO A 910 " ideal model delta sigma weight residual 1.419 1.370 0.049 2.00e-02 2.50e+03 6.00e+00 bond pdb=" CB SRO A 910 " pdb=" CG SRO A 910 " ideal model delta sigma weight residual 1.498 1.527 -0.029 2.00e-02 2.50e+03 2.14e+00 ... (remaining 6342 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 8270 1.10 - 2.20: 212 2.20 - 3.30: 61 3.30 - 4.40: 51 4.40 - 5.50: 15 Bond angle restraints: 8609 Sorted by residual: angle pdb=" C ALA C 74 " pdb=" N ALA C 75 " pdb=" CA ALA C 75 " ideal model delta sigma weight residual 121.54 126.26 -4.72 1.91e+00 2.74e-01 6.10e+00 angle pdb=" N SER B 122 " pdb=" CA SER B 122 " pdb=" C SER B 122 " ideal model delta sigma weight residual 111.11 113.76 -2.65 1.20e+00 6.94e-01 4.88e+00 angle pdb=" N PHE A 287 " pdb=" CA PHE A 287 " pdb=" C PHE A 287 " ideal model delta sigma weight residual 109.81 114.29 -4.48 2.21e+00 2.05e-01 4.11e+00 angle pdb=" N ILE B 67 " pdb=" CA ILE B 67 " pdb=" C ILE B 67 " ideal model delta sigma weight residual 111.48 109.58 1.90 9.40e-01 1.13e+00 4.09e+00 angle pdb=" N PRO A 403 " pdb=" CA PRO A 403 " pdb=" C PRO A 403 " ideal model delta sigma weight residual 114.68 112.59 2.09 1.04e+00 9.25e-01 4.03e+00 ... (remaining 8604 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.32: 3288 16.32 - 32.65: 269 32.65 - 48.97: 40 48.97 - 65.30: 6 65.30 - 81.62: 6 Dihedral angle restraints: 3609 sinusoidal: 1403 harmonic: 2206 Sorted by residual: dihedral pdb=" CA ASP B 76 " pdb=" CB ASP B 76 " pdb=" CG ASP B 76 " pdb=" OD1 ASP B 76 " ideal model delta sinusoidal sigma weight residual -30.00 -82.18 52.18 1 2.00e+01 2.50e-03 9.28e+00 dihedral pdb=" CA LEU A 261 " pdb=" CB LEU A 261 " pdb=" CG LEU A 261 " pdb=" CD1 LEU A 261 " ideal model delta sinusoidal sigma weight residual 180.00 132.97 47.03 3 1.50e+01 4.44e-03 8.43e+00 dihedral pdb=" CA LEU B 23 " pdb=" CB LEU B 23 " pdb=" CG LEU B 23 " pdb=" CD1 LEU B 23 " ideal model delta sinusoidal sigma weight residual 180.00 134.08 45.92 3 1.50e+01 4.44e-03 8.25e+00 ... (remaining 3606 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 912 0.087 - 0.175: 30 0.175 - 0.262: 0 0.262 - 0.350: 0 0.350 - 0.437: 1 Chirality restraints: 943 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-02 2.50e+03 4.78e+02 chirality pdb=" CA ILE C 41 " pdb=" N ILE C 41 " pdb=" C ILE C 41 " pdb=" CB ILE C 41 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 chirality pdb=" CA VAL C 82 " pdb=" N VAL C 82 " pdb=" C VAL C 82 " pdb=" CB VAL C 82 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 940 not shown) Planarity restraints: 1050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 338 " -0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO A 339 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 287 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO A 288 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 288 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 288 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 498 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO A 499 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 499 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 499 " 0.016 5.00e-02 4.00e+02 ... (remaining 1047 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1976 2.83 - 3.35: 5574 3.35 - 3.86: 9998 3.86 - 4.38: 11021 4.38 - 4.90: 19411 Nonbonded interactions: 47980 Sorted by model distance: nonbonded pdb=" O SER A 214 " pdb=" OG SER A 214 " model vdw 2.309 3.040 nonbonded pdb=" O SER B 49 " pdb=" OG SER B 49 " model vdw 2.311 3.040 nonbonded pdb=" OH TYR A 110 " pdb=" O ALA A 398 " model vdw 2.321 3.040 nonbonded pdb=" O SER A 190 " pdb=" OG SER A 190 " model vdw 2.330 3.040 nonbonded pdb=" NE2 GLN C 114 " pdb=" O SER C 119 " model vdw 2.345 3.120 ... (remaining 47975 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 4.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.570 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 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 : 0.003 0.065 6353 Z= 0.135 Angle : 0.681 22.061 8621 Z= 0.299 Chirality : 0.040 0.437 943 Planarity : 0.003 0.037 1049 Dihedral : 11.854 81.620 2200 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.52 (0.26), residues: 761 helix: -1.06 (0.24), residues: 349 sheet: -2.81 (0.55), residues: 76 loop : -3.68 (0.25), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 38 TYR 0.008 0.001 TYR A 175 PHE 0.007 0.001 PHE A 287 TRP 0.003 0.000 TRP A 317 HIS 0.002 0.000 HIS C 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 ( 6347) covalent geometry : angle 0.55946 / 0.27 ( 8609) SS BOND : bond 0.00127 / 0.06 ( 3) SS BOND : angle 0.21786 / 0.13 ( 6) hydrogen bonds : bond 0.17743 / 10.60 ( 268) hydrogen bonds : angle 5.67003 / 3.87 ( 756) Misc. bond : bond 0.00024 / 0.01 ( 1) link_BETA1-4 : bond 0.06547 / 3.45 ( 1) link_BETA1-4 : angle 20.83721 / 11.23 ( 3) link_NAG-ASN : bond 0.00129 / 0.07 ( 1) link_NAG-ASN : angle 1.20753 / 0.66 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 542 VAL cc_start: 0.8386 (m) cc_final: 0.8004 (p) REVERT: C 62 GLN cc_start: 0.8423 (tt0) cc_final: 0.8184 (tt0) REVERT: C 114 GLN cc_start: 0.8014 (pp30) cc_final: 0.7472 (pp30) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.0774 time to fit residues: 16.3248 Evaluate side-chains 102 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 GLN A 254 GLN A 332 GLN B 25 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.161662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.139334 restraints weight = 9098.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.141131 restraints weight = 6745.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.142327 restraints weight = 5351.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.142984 restraints weight = 4727.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.143766 restraints weight = 4233.079| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6353 Z= 0.177 Angle : 0.601 8.234 8621 Z= 0.303 Chirality : 0.042 0.201 943 Planarity : 0.004 0.040 1049 Dihedral : 5.891 66.328 886 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.80 % Allowed : 13.20 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.29), residues: 761 helix: -0.15 (0.27), residues: 350 sheet: -2.62 (0.57), residues: 84 loop : -3.00 (0.30), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 59 TYR 0.023 0.002 TYR A 312 PHE 0.021 0.002 PHE A 531 TRP 0.014 0.001 TRP A 537 HIS 0.002 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 ( 6347) covalent geometry : angle 0.59424 / 0.30 ( 8609) SS BOND : bond 0.00306 / 0.16 ( 3) SS BOND : angle 0.99467 / 0.52 ( 6) hydrogen bonds : bond 0.03609 / 2.24 ( 268) hydrogen bonds : angle 4.15652 / 2.87 ( 756) Misc. bond : bond 0.00029 / 0.02 ( 1) link_BETA1-4 : bond 0.02548 / 1.34 ( 1) link_BETA1-4 : angle 4.43513 / 2.33 ( 3) link_NAG-ASN : bond 0.00414 / 0.22 ( 1) link_NAG-ASN : angle 1.83808 / 0.99 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 295 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8133 (tt) REVERT: C 114 GLN cc_start: 0.8489 (pp30) cc_final: 0.7842 (pp30) outliers start: 18 outliers final: 11 residues processed: 111 average time/residue: 0.0733 time to fit residues: 10.8970 Evaluate side-chains 107 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 41 optimal weight: 0.0770 chunk 42 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 38 optimal weight: 0.3980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.157144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.135682 restraints weight = 9048.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.135725 restraints weight = 8063.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.137723 restraints weight = 7638.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.137944 restraints weight = 5387.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.138451 restraints weight = 4967.043| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6353 Z= 0.126 Angle : 0.530 7.608 8621 Z= 0.265 Chirality : 0.040 0.131 943 Planarity : 0.003 0.039 1049 Dihedral : 5.559 58.493 886 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.17 % Allowed : 15.68 % Favored : 82.14 % 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: -1.94 (0.30), residues: 761 helix: 0.25 (0.28), residues: 349 sheet: -2.29 (0.56), residues: 89 loop : -2.77 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 85 TYR 0.012 0.001 TYR A 175 PHE 0.027 0.001 PHE A 531 TRP 0.010 0.001 TRP B 130 HIS 0.002 0.001 HIS C 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 6347) covalent geometry : angle 0.52368 / 0.26 ( 8609) SS BOND : bond 0.00208 / 0.11 ( 3) SS BOND : angle 0.68259 / 0.37 ( 6) hydrogen bonds : bond 0.03186 / 1.97 ( 268) hydrogen bonds : angle 3.95999 / 2.71 ( 756) Misc. bond : bond 0.00105 / 0.06 ( 1) link_BETA1-4 : bond 0.01929 / 1.02 ( 1) link_BETA1-4 : angle 4.11969 / 2.17 ( 3) link_NAG-ASN : bond 0.00234 / 0.12 ( 1) link_NAG-ASN : angle 1.21039 / 0.66 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 295 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8261 (tt) REVERT: A 423 PHE cc_start: 0.7273 (m-80) cc_final: 0.6879 (m-10) REVERT: B 101 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7983 (tm-30) REVERT: C 114 GLN cc_start: 0.8621 (pp30) cc_final: 0.7892 (pp30) outliers start: 14 outliers final: 10 residues processed: 106 average time/residue: 0.0687 time to fit residues: 10.2321 Evaluate side-chains 103 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain C residue 127 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN C 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.146319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.126742 restraints weight = 9192.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.124974 restraints weight = 9917.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.126712 restraints weight = 9733.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.126992 restraints weight = 7459.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.127060 restraints weight = 6821.715| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 6353 Z= 0.182 Angle : 0.603 9.148 8621 Z= 0.307 Chirality : 0.042 0.157 943 Planarity : 0.004 0.039 1049 Dihedral : 5.529 58.507 886 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 4.19 % Allowed : 17.08 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.29), residues: 761 helix: 0.18 (0.27), residues: 353 sheet: -2.19 (0.56), residues: 85 loop : -2.55 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 234 TYR 0.016 0.002 TYR A 185 PHE 0.025 0.002 PHE A 531 TRP 0.012 0.001 TRP B 130 HIS 0.004 0.001 HIS C 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.18 ( 6347) covalent geometry : angle 0.59767 / 0.31 ( 8609) SS BOND : bond 0.00428 / 0.22 ( 3) SS BOND : angle 1.20199 / 0.64 ( 6) hydrogen bonds : bond 0.03523 / 2.24 ( 268) hydrogen bonds : angle 4.08628 / 2.78 ( 756) Misc. bond : bond 0.00224 / 0.12 ( 1) link_BETA1-4 : bond 0.01522 / 0.80 ( 1) link_BETA1-4 : angle 3.71899 / 1.96 ( 3) link_NAG-ASN : bond 0.00117 / 0.06 ( 1) link_NAG-ASN : angle 1.18356 / 0.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 271 TRP cc_start: 0.6830 (OUTLIER) cc_final: 0.6610 (t60) REVERT: A 295 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8399 (tt) REVERT: C 114 GLN cc_start: 0.9037 (pp30) cc_final: 0.8692 (pp30) outliers start: 27 outliers final: 16 residues processed: 120 average time/residue: 0.0584 time to fit residues: 9.7230 Evaluate side-chains 105 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 535 TRP Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 127 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 57 optimal weight: 0.0770 chunk 31 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 11 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.147825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.125035 restraints weight = 9281.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.123707 restraints weight = 8110.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.125918 restraints weight = 8481.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.126227 restraints weight = 6082.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.126691 restraints weight = 5662.994| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6353 Z= 0.128 Angle : 0.550 8.019 8621 Z= 0.278 Chirality : 0.041 0.174 943 Planarity : 0.004 0.039 1049 Dihedral : 5.206 55.573 886 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.48 % Allowed : 19.57 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.58 (0.30), residues: 761 helix: 0.42 (0.28), residues: 350 sheet: -2.06 (0.56), residues: 85 loop : -2.44 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 234 TYR 0.029 0.001 TYR B 46 PHE 0.025 0.001 PHE A 531 TRP 0.009 0.001 TRP B 130 HIS 0.002 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 6347) covalent geometry : angle 0.54543 / 0.28 ( 8609) SS BOND : bond 0.00321 / 0.16 ( 3) SS BOND : angle 0.81528 / 0.43 ( 6) hydrogen bonds : bond 0.03110 / 1.97 ( 268) hydrogen bonds : angle 4.01582 / 2.73 ( 756) Misc. bond : bond 0.00155 / 0.08 ( 1) link_BETA1-4 : bond 0.01796 / 0.95 ( 1) link_BETA1-4 : angle 3.67708 / 1.94 ( 3) link_NAG-ASN : bond 0.00157 / 0.08 ( 1) link_NAG-ASN : angle 0.91886 / 0.52 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 440 PHE cc_start: 0.8447 (m-10) cc_final: 0.8189 (m-80) REVERT: A 548 PHE cc_start: 0.8469 (t80) cc_final: 0.8222 (t80) REVERT: C 37 GLN cc_start: 0.8180 (mp10) cc_final: 0.7952 (mp10) REVERT: C 114 GLN cc_start: 0.8937 (pp30) cc_final: 0.8582 (pp30) outliers start: 16 outliers final: 14 residues processed: 107 average time/residue: 0.0648 time to fit residues: 9.7697 Evaluate side-chains 100 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain C residue 127 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 30 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.0970 chunk 43 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.146174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.120943 restraints weight = 9116.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.123365 restraints weight = 6588.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.124682 restraints weight = 5303.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.126049 restraints weight = 4626.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.126591 restraints weight = 4173.233| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6353 Z= 0.152 Angle : 0.569 9.321 8621 Z= 0.285 Chirality : 0.041 0.152 943 Planarity : 0.004 0.039 1049 Dihedral : 5.020 44.480 886 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 3.73 % Allowed : 20.19 % Favored : 76.09 % 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: -1.46 (0.30), residues: 761 helix: 0.36 (0.27), residues: 355 sheet: -1.77 (0.58), residues: 85 loop : -2.29 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 234 TYR 0.022 0.001 TYR A 142 PHE 0.029 0.002 PHE A 531 TRP 0.008 0.001 TRP B 130 HIS 0.002 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 ( 6347) covalent geometry : angle 0.56433 / 0.28 ( 8609) SS BOND : bond 0.00402 / 0.21 ( 3) SS BOND : angle 1.03147 / 0.54 ( 6) hydrogen bonds : bond 0.03199 / 2.03 ( 268) hydrogen bonds : angle 4.04064 / 2.74 ( 756) Misc. bond : bond 0.00230 / 0.12 ( 1) link_BETA1-4 : bond 0.01859 / 0.98 ( 1) link_BETA1-4 : angle 3.60862 / 1.90 ( 3) link_NAG-ASN : bond 0.00008 / 0.00 ( 1) link_NAG-ASN : angle 0.92305 / 0.51 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 TRP cc_start: 0.6774 (OUTLIER) cc_final: 0.6539 (t60) REVERT: A 295 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8285 (tt) REVERT: A 440 PHE cc_start: 0.8493 (m-10) cc_final: 0.8250 (m-80) REVERT: A 542 VAL cc_start: 0.8692 (m) cc_final: 0.8465 (p) REVERT: C 37 GLN cc_start: 0.8240 (mp10) cc_final: 0.7990 (mp10) REVERT: C 102 MET cc_start: 0.7070 (tmm) cc_final: 0.6665 (ttp) outliers start: 24 outliers final: 20 residues processed: 110 average time/residue: 0.0603 time to fit residues: 9.2309 Evaluate side-chains 109 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 127 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 40 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.143872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.118526 restraints weight = 9205.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.120949 restraints weight = 6648.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.122449 restraints weight = 5323.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.123488 restraints weight = 4616.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.124473 restraints weight = 4177.465| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6353 Z= 0.148 Angle : 0.557 8.823 8621 Z= 0.280 Chirality : 0.041 0.155 943 Planarity : 0.004 0.039 1049 Dihedral : 4.850 26.918 886 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.88 % Allowed : 21.43 % Favored : 74.69 % 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: -1.27 (0.31), residues: 761 helix: 0.49 (0.28), residues: 351 sheet: -1.70 (0.58), residues: 85 loop : -2.11 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 234 TYR 0.018 0.002 TYR A 142 PHE 0.026 0.002 PHE A 531 TRP 0.009 0.001 TRP B 130 HIS 0.002 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 6347) covalent geometry : angle 0.55268 / 0.28 ( 8609) SS BOND : bond 0.00401 / 0.21 ( 3) SS BOND : angle 0.90303 / 0.47 ( 6) hydrogen bonds : bond 0.03188 / 2.03 ( 268) hydrogen bonds : angle 4.05206 / 2.76 ( 756) Misc. bond : bond 0.00089 / 0.05 ( 1) link_BETA1-4 : bond 0.01892 / 1.00 ( 1) link_BETA1-4 : angle 3.53650 / 1.86 ( 3) link_NAG-ASN : bond 0.00103 / 0.05 ( 1) link_NAG-ASN : angle 0.86026 / 0.48 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.8629 (mmt-90) cc_final: 0.8416 (mmt-90) REVERT: A 271 TRP cc_start: 0.6784 (OUTLIER) cc_final: 0.6559 (t60) REVERT: A 295 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8198 (tt) REVERT: A 542 VAL cc_start: 0.8801 (m) cc_final: 0.8591 (p) REVERT: B 100 MET cc_start: 0.8953 (ttt) cc_final: 0.8694 (ttt) REVERT: C 102 MET cc_start: 0.6986 (tmm) cc_final: 0.6646 (ttp) REVERT: C 103 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7492 (mt-10) outliers start: 25 outliers final: 20 residues processed: 109 average time/residue: 0.0625 time to fit residues: 9.5876 Evaluate side-chains 110 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 48 optimal weight: 0.0970 chunk 21 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 63 optimal weight: 0.0870 chunk 29 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.144391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.121567 restraints weight = 9190.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.121775 restraints weight = 7507.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.123896 restraints weight = 6906.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.123853 restraints weight = 5020.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.124152 restraints weight = 4876.336| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6353 Z= 0.127 Angle : 0.568 9.208 8621 Z= 0.283 Chirality : 0.040 0.144 943 Planarity : 0.003 0.039 1049 Dihedral : 4.654 25.224 886 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 2.80 % Allowed : 22.67 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.31), residues: 761 helix: 0.59 (0.28), residues: 354 sheet: -1.57 (0.59), residues: 85 loop : -2.01 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 234 TYR 0.013 0.001 TYR A 175 PHE 0.024 0.001 PHE A 531 TRP 0.008 0.001 TRP A 573 HIS 0.005 0.001 HIS C 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 6347) covalent geometry : angle 0.56434 / 0.28 ( 8609) SS BOND : bond 0.00325 / 0.17 ( 3) SS BOND : angle 0.74130 / 0.39 ( 6) hydrogen bonds : bond 0.03071 / 1.95 ( 268) hydrogen bonds : angle 4.02353 / 2.74 ( 756) Misc. bond : bond 0.00090 / 0.05 ( 1) link_BETA1-4 : bond 0.01849 / 0.97 ( 1) link_BETA1-4 : angle 3.41953 / 1.80 ( 3) link_NAG-ASN : bond 0.00050 / 0.03 ( 1) link_NAG-ASN : angle 0.75447 / 0.42 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 271 TRP cc_start: 0.6760 (OUTLIER) cc_final: 0.6544 (t60) REVERT: A 542 VAL cc_start: 0.8772 (m) cc_final: 0.8552 (p) REVERT: B 100 MET cc_start: 0.8876 (ttt) cc_final: 0.8616 (ttt) outliers start: 18 outliers final: 17 residues processed: 106 average time/residue: 0.0667 time to fit residues: 9.9341 Evaluate side-chains 107 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 57 optimal weight: 0.1980 chunk 50 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 20 GLN C 100 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.143306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.121763 restraints weight = 9161.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.121326 restraints weight = 8022.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.123334 restraints weight = 7956.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.123416 restraints weight = 5783.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.123826 restraints weight = 5398.308| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6353 Z= 0.149 Angle : 0.592 9.240 8621 Z= 0.295 Chirality : 0.041 0.155 943 Planarity : 0.004 0.039 1049 Dihedral : 4.725 26.184 886 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 3.73 % Allowed : 22.36 % Favored : 73.91 % 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: -1.16 (0.31), residues: 761 helix: 0.49 (0.28), residues: 356 sheet: -1.45 (0.60), residues: 85 loop : -2.03 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 234 TYR 0.013 0.001 TYR A 175 PHE 0.021 0.002 PHE A 531 TRP 0.008 0.001 TRP B 130 HIS 0.003 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 6347) covalent geometry : angle 0.58837 / 0.29 ( 8609) SS BOND : bond 0.00407 / 0.21 ( 3) SS BOND : angle 0.99017 / 0.52 ( 6) hydrogen bonds : bond 0.03211 / 2.04 ( 268) hydrogen bonds : angle 4.08184 / 2.78 ( 756) Misc. bond : bond 0.00075 / 0.04 ( 1) link_BETA1-4 : bond 0.02000 / 1.05 ( 1) link_BETA1-4 : angle 3.44975 / 1.82 ( 3) link_NAG-ASN : bond 0.00040 / 0.02 ( 1) link_NAG-ASN : angle 0.86080 / 0.47 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 295 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8286 (tt) REVERT: B 100 MET cc_start: 0.8869 (ttt) cc_final: 0.8606 (ttt) outliers start: 24 outliers final: 19 residues processed: 109 average time/residue: 0.0537 time to fit residues: 8.5998 Evaluate side-chains 104 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 0.0170 chunk 7 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.143083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.119369 restraints weight = 9181.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.119985 restraints weight = 7073.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.121118 restraints weight = 6057.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.121824 restraints weight = 5355.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.122370 restraints weight = 4782.185| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6353 Z= 0.149 Angle : 0.606 9.354 8621 Z= 0.303 Chirality : 0.041 0.161 943 Planarity : 0.004 0.039 1049 Dihedral : 4.753 26.311 886 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 3.42 % Allowed : 23.14 % Favored : 73.45 % 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: -1.11 (0.31), residues: 761 helix: 0.51 (0.28), residues: 356 sheet: -1.32 (0.60), residues: 89 loop : -2.02 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 234 TYR 0.017 0.001 TYR A 142 PHE 0.021 0.002 PHE A 531 TRP 0.015 0.001 TRP B 130 HIS 0.002 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 6347) covalent geometry : angle 0.60214 / 0.30 ( 8609) SS BOND : bond 0.00366 / 0.19 ( 3) SS BOND : angle 0.93366 / 0.49 ( 6) hydrogen bonds : bond 0.03203 / 2.05 ( 268) hydrogen bonds : angle 4.08901 / 2.78 ( 756) Misc. bond : bond 0.00148 / 0.08 ( 1) link_BETA1-4 : bond 0.01835 / 0.97 ( 1) link_BETA1-4 : angle 3.31920 / 1.75 ( 3) link_NAG-ASN : bond 0.00015 / 0.01 ( 1) link_NAG-ASN : angle 0.83611 / 0.45 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 295 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8208 (tt) REVERT: B 100 MET cc_start: 0.8885 (ttt) cc_final: 0.8630 (ttt) outliers start: 22 outliers final: 21 residues processed: 106 average time/residue: 0.0568 time to fit residues: 8.6058 Evaluate side-chains 107 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 72 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.141624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.118223 restraints weight = 9176.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.118410 restraints weight = 7557.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.120387 restraints weight = 7078.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.120593 restraints weight = 5138.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.121261 restraints weight = 4927.529| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.5704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6353 Z= 0.181 Angle : 0.634 9.315 8621 Z= 0.319 Chirality : 0.042 0.166 943 Planarity : 0.004 0.038 1049 Dihedral : 5.015 28.574 886 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 4.04 % Allowed : 22.83 % Favored : 73.14 % 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: -1.25 (0.31), residues: 761 helix: 0.41 (0.27), residues: 355 sheet: -1.60 (0.57), residues: 95 loop : -2.04 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 523 TYR 0.014 0.002 TYR B 46 PHE 0.020 0.002 PHE A 531 TRP 0.009 0.001 TRP B 130 HIS 0.007 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 ( 6347) covalent geometry : angle 0.63053 / 0.32 ( 8609) SS BOND : bond 0.00423 / 0.22 ( 3) SS BOND : angle 1.08096 / 0.57 ( 6) hydrogen bonds : bond 0.03405 / 2.18 ( 268) hydrogen bonds : angle 4.16824 / 2.84 ( 756) Misc. bond : bond 0.00146 / 0.08 ( 1) link_BETA1-4 : bond 0.01754 / 0.92 ( 1) link_BETA1-4 : angle 3.22739 / 1.70 ( 3) link_NAG-ASN : bond 0.00077 / 0.04 ( 1) link_NAG-ASN : angle 0.93620 / 0.50 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1034.74 seconds wall clock time: 18 minutes 40.17 seconds (1120.17 seconds total)