Starting phenix.real_space_refine on Tue Mar 11 18:08:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7li9_23364/03_2025/7li9_23364.cif Found real_map, /net/cci-nas-00/data/ceres_data/7li9_23364/03_2025/7li9_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7li9_23364/03_2025/7li9_23364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7li9_23364/03_2025/7li9_23364.map" model { file = "/net/cci-nas-00/data/ceres_data/7li9_23364/03_2025/7li9_23364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7li9_23364/03_2025/7li9_23364.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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 dihedrals: 6 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: 5.66, per 1000 atoms: 0.92 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: 1.63 Conformation dependent library (CDL) restraints added in 837.2 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: 0.58 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: 1.57 Time building geometry restraints manager: 1.84 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 - 20.59: 3431 20.59 - 41.17: 187 41.17 - 61.76: 19 61.76 - 82.35: 6 82.35 - 102.94: 8 Dihedral angle restraints: 3651 sinusoidal: 1445 harmonic: 2206 Sorted by residual: dihedral pdb=" C1 NAG D 2 " pdb=" C2 NAG D 2 " pdb=" C3 NAG D 2 " pdb=" O3 NAG D 2 " ideal model delta sinusoidal sigma weight residual -175.09 -72.15 -102.94 1 3.00e+01 1.11e-03 1.31e+01 dihedral pdb=" C1 NAG D 2 " pdb=" C2 NAG D 2 " pdb=" C3 NAG D 2 " pdb=" C4 NAG D 2 " ideal model delta sinusoidal sigma weight residual -52.39 49.80 -102.19 1 3.00e+01 1.11e-03 1.29e+01 dihedral pdb=" N2 NAG D 2 " pdb=" C2 NAG D 2 " pdb=" C3 NAG D 2 " pdb=" O3 NAG D 2 " ideal model delta sinusoidal sigma weight residual 62.25 164.33 -102.08 1 3.00e+01 1.11e-03 1.29e+01 ... (remaining 3648 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: 7.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.350 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 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 0.053 6347 Z= 0.172 Angle : 0.559 5.496 8609 Z= 0.269 Chirality : 0.040 0.437 943 Planarity : 0.003 0.037 1049 Dihedral : 13.558 102.936 2242 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.39 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (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 TRP 0.003 0.000 TRP A 317 HIS 0.002 0.000 HIS C 100 PHE 0.007 0.001 PHE A 287 TYR 0.008 0.001 TYR A 175 ARG 0.001 0.000 ARG C 38 *********************** 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 : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 542 VAL cc_start: 0.8386 (m) cc_final: 0.8005 (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: 0.2048 time to fit residues: 42.2320 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 : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 58 optimal weight: 0.3980 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3875 r_free = 0.3875 target = 0.162832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.140748 restraints weight = 8982.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.141946 restraints weight = 6884.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.143537 restraints weight = 5632.738| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6347 Z= 0.242 Angle : 0.611 8.616 8609 Z= 0.306 Chirality : 0.042 0.202 943 Planarity : 0.004 0.039 1049 Dihedral : 8.748 67.518 928 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.33 % Allowed : 13.20 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.29), residues: 761 helix: -0.08 (0.27), residues: 350 sheet: -2.60 (0.58), residues: 84 loop : -2.98 (0.30), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 537 HIS 0.002 0.001 HIS A 235 PHE 0.022 0.002 PHE A 531 TYR 0.025 0.002 TYR A 312 ARG 0.004 0.001 ARG B 59 *********************** 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 116 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.8662 (mmt-90) cc_final: 0.8284 (mmm-85) REVERT: A 295 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8159 (tt) REVERT: C 114 GLN cc_start: 0.8439 (pp30) cc_final: 0.7831 (pp30) outliers start: 15 outliers final: 10 residues processed: 108 average time/residue: 0.1802 time to fit residues: 25.9656 Evaluate side-chains 105 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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 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 62 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 6 optimal weight: 0.0040 chunk 45 optimal weight: 4.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.150874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.127744 restraints weight = 9150.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.128423 restraints weight = 7051.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.129083 restraints weight = 6286.426| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 6347 Z= 0.257 Angle : 0.583 8.333 8609 Z= 0.293 Chirality : 0.042 0.139 943 Planarity : 0.004 0.040 1049 Dihedral : 6.537 55.412 928 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.42 % Allowed : 15.84 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.30), residues: 761 helix: 0.10 (0.28), residues: 348 sheet: -2.26 (0.56), residues: 85 loop : -2.72 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 130 HIS 0.002 0.001 HIS A 235 PHE 0.024 0.002 PHE A 531 TYR 0.014 0.002 TYR A 185 ARG 0.007 0.001 ARG C 85 *********************** 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 123 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.706 Fit side-chains REVERT: A 295 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8357 (tt) REVERT: C 114 GLN cc_start: 0.8879 (pp30) cc_final: 0.8060 (pp30) REVERT: C 116 LYS cc_start: 0.6603 (mttt) cc_final: 0.6022 (mttt) outliers start: 22 outliers final: 15 residues processed: 114 average time/residue: 0.1967 time to fit residues: 30.4414 Evaluate side-chains 105 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 295 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 522 CYS Chi-restraints excluded: chain A residue 535 TRP Chi-restraints excluded: chain A residue 547 LEU 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 47 GLU 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 33 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 42 optimal weight: 0.2980 chunk 68 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.150326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.125953 restraints weight = 9297.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.126864 restraints weight = 6763.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.128153 restraints weight = 5559.590| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6347 Z= 0.196 Angle : 0.534 7.931 8609 Z= 0.268 Chirality : 0.040 0.136 943 Planarity : 0.003 0.039 1049 Dihedral : 5.821 53.051 928 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.48 % Allowed : 19.41 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.30), residues: 761 helix: 0.39 (0.28), residues: 349 sheet: -2.35 (0.52), residues: 94 loop : -2.46 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 130 HIS 0.001 0.001 HIS A 240 PHE 0.028 0.001 PHE A 531 TYR 0.027 0.001 TYR B 46 ARG 0.006 0.000 ARG A 234 *********************** 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 113 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.618 Fit side-chains REVERT: A 135 MET cc_start: 0.8552 (ttp) cc_final: 0.8333 (tmm) REVERT: C 37 GLN cc_start: 0.8182 (mp10) cc_final: 0.7902 (mp10) REVERT: C 114 GLN cc_start: 0.8895 (pp30) cc_final: 0.8575 (pp30) outliers start: 16 outliers final: 10 residues processed: 108 average time/residue: 0.1706 time to fit residues: 25.0859 Evaluate side-chains 99 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 549 LEU 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 12 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 chunk 58 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 55 optimal weight: 0.0040 chunk 3 optimal weight: 0.9980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.150131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.127662 restraints weight = 9155.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.126512 restraints weight = 7904.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.128146 restraints weight = 8649.460| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6347 Z= 0.185 Angle : 0.538 8.262 8609 Z= 0.267 Chirality : 0.040 0.137 943 Planarity : 0.003 0.038 1049 Dihedral : 5.142 43.183 928 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.64 % Allowed : 20.50 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.30), residues: 761 helix: 0.52 (0.28), residues: 349 sheet: -1.87 (0.57), residues: 85 loop : -2.32 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 130 HIS 0.001 0.001 HIS A 235 PHE 0.032 0.001 PHE A 531 TYR 0.020 0.001 TYR A 142 ARG 0.005 0.000 ARG A 234 *********************** 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: 17 poor density : 95 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: A 135 MET cc_start: 0.8630 (ttp) cc_final: 0.8414 (tmm) REVERT: A 548 PHE cc_start: 0.8393 (t80) cc_final: 0.8186 (t80) REVERT: B 100 MET cc_start: 0.8771 (ttt) cc_final: 0.8497 (ttt) REVERT: C 102 MET cc_start: 0.6930 (tmm) cc_final: 0.6690 (ttp) REVERT: C 114 GLN cc_start: 0.8900 (pp30) cc_final: 0.8608 (pp30) outliers start: 17 outliers final: 12 residues processed: 107 average time/residue: 0.1503 time to fit residues: 22.2457 Evaluate side-chains 98 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 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 547 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain C residue 40 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 55 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.142373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.119746 restraints weight = 9216.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.118935 restraints weight = 8085.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.119906 restraints weight = 8629.059| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6347 Z= 0.295 Angle : 0.610 10.336 8609 Z= 0.307 Chirality : 0.043 0.149 943 Planarity : 0.004 0.038 1049 Dihedral : 5.329 33.493 928 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 3.88 % Allowed : 20.19 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.30), residues: 761 helix: 0.29 (0.27), residues: 353 sheet: -1.77 (0.59), residues: 85 loop : -2.19 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 130 HIS 0.002 0.001 HIS A 235 PHE 0.027 0.002 PHE A 531 TYR 0.017 0.002 TYR A 142 ARG 0.008 0.001 ARG A 234 *********************** 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 118 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 295 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8251 (tt) REVERT: C 102 MET cc_start: 0.7059 (tmm) cc_final: 0.6737 (ttp) outliers start: 25 outliers final: 19 residues processed: 111 average time/residue: 0.1418 time to fit residues: 22.2452 Evaluate side-chains 102 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 210 THR 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 295 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 362 LEU 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 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 C residue 40 THR 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 58 optimal weight: 0.2980 chunk 8 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 40 optimal weight: 0.5980 chunk 52 optimal weight: 0.1980 chunk 15 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.144923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.122631 restraints weight = 9162.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.122411 restraints weight = 8240.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.124207 restraints weight = 8244.539| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.5147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6347 Z= 0.186 Angle : 0.557 9.211 8609 Z= 0.279 Chirality : 0.040 0.137 943 Planarity : 0.003 0.038 1049 Dihedral : 4.985 33.177 928 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 2.64 % Allowed : 21.89 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.31), residues: 761 helix: 0.49 (0.28), residues: 353 sheet: -1.64 (0.58), residues: 85 loop : -2.10 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 573 HIS 0.002 0.001 HIS A 235 PHE 0.024 0.001 PHE A 531 TYR 0.014 0.001 TYR A 175 ARG 0.005 0.000 ARG A 234 *********************** 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 106 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 20 GLN cc_start: 0.7345 (mm-40) cc_final: 0.7130 (mm110) REVERT: B 100 MET cc_start: 0.8851 (ttt) cc_final: 0.8595 (ttt) REVERT: C 37 GLN cc_start: 0.8407 (mm-40) cc_final: 0.8133 (mp10) REVERT: C 102 MET cc_start: 0.6948 (tmm) cc_final: 0.6684 (ttp) outliers start: 17 outliers final: 14 residues processed: 102 average time/residue: 0.1559 time to fit residues: 22.0735 Evaluate side-chains 98 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 327 ILE 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 549 LEU Chi-restraints excluded: chain A residue 583 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 0.0470 chunk 49 optimal weight: 0.6980 chunk 41 optimal weight: 0.0870 chunk 33 optimal weight: 0.6980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.145042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.122866 restraints weight = 9069.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.122218 restraints weight = 7996.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.124463 restraints weight = 7923.142| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6347 Z= 0.185 Angle : 0.575 9.505 8609 Z= 0.287 Chirality : 0.040 0.171 943 Planarity : 0.004 0.038 1049 Dihedral : 4.791 32.810 928 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.64 % Allowed : 23.29 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.31), residues: 761 helix: 0.59 (0.28), residues: 351 sheet: -1.62 (0.58), residues: 85 loop : -2.03 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 130 HIS 0.001 0.001 HIS A 240 PHE 0.022 0.001 PHE A 531 TYR 0.018 0.001 TYR A 142 ARG 0.009 0.000 ARG A 234 *********************** 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 108 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.583 Fit side-chains revert: symmetry clash REVERT: B 100 MET cc_start: 0.8842 (ttt) cc_final: 0.8595 (ttt) REVERT: C 103 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7433 (mt-10) outliers start: 17 outliers final: 16 residues processed: 104 average time/residue: 0.1895 time to fit residues: 27.5727 Evaluate side-chains 101 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 386 MET Chi-restraints excluded: chain A residue 393 ASP 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 0.0870 chunk 43 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.142560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.117248 restraints weight = 9268.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.119571 restraints weight = 6826.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.120689 restraints weight = 5553.145| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.5468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6347 Z= 0.247 Angle : 0.610 9.185 8609 Z= 0.305 Chirality : 0.042 0.154 943 Planarity : 0.004 0.038 1049 Dihedral : 5.017 32.832 928 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 3.11 % Allowed : 22.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.31), residues: 761 helix: 0.46 (0.28), residues: 354 sheet: -1.59 (0.59), residues: 85 loop : -1.96 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 130 HIS 0.002 0.001 HIS C 100 PHE 0.020 0.002 PHE A 531 TYR 0.015 0.001 TYR A 175 ARG 0.009 0.000 ARG A 234 *********************** 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 109 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: A 295 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8277 (tt) REVERT: B 100 MET cc_start: 0.8936 (ttt) cc_final: 0.8697 (ttt) outliers start: 20 outliers final: 18 residues processed: 104 average time/residue: 0.1494 time to fit residues: 21.7536 Evaluate side-chains 103 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 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 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 549 LEU Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain C residue 40 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 17 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 9 optimal weight: 0.1980 chunk 48 optimal weight: 0.0970 chunk 64 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN A 354 ASN B 20 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.144664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.122016 restraints weight = 9274.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.122388 restraints weight = 7977.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.124364 restraints weight = 7230.375| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.5485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6347 Z= 0.192 Angle : 0.587 9.937 8609 Z= 0.294 Chirality : 0.041 0.141 943 Planarity : 0.004 0.038 1049 Dihedral : 4.929 32.902 928 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.64 % Allowed : 23.29 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.31), residues: 761 helix: 0.60 (0.28), residues: 353 sheet: -1.51 (0.59), residues: 85 loop : -1.92 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 326 HIS 0.001 0.001 HIS A 240 PHE 0.019 0.001 PHE A 531 TYR 0.016 0.001 TYR B 129 ARG 0.009 0.000 ARG A 234 ********************** 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 108 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.704 Fit side-chains REVERT: B 100 MET cc_start: 0.8852 (ttt) cc_final: 0.8606 (ttt) outliers start: 17 outliers final: 16 residues processed: 105 average time/residue: 0.1590 time to fit residues: 23.3049 Evaluate side-chains 103 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 386 MET Chi-restraints excluded: chain A residue 393 ASP 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 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 71 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 0.0970 chunk 60 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.141045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.117969 restraints weight = 9430.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.117860 restraints weight = 7698.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.119423 restraints weight = 7212.350| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.5721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6347 Z= 0.277 Angle : 0.637 9.667 8609 Z= 0.321 Chirality : 0.043 0.154 943 Planarity : 0.004 0.038 1049 Dihedral : 5.159 32.937 928 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 2.80 % Allowed : 24.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.31), residues: 761 helix: 0.40 (0.27), residues: 355 sheet: -1.42 (0.60), residues: 85 loop : -1.96 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 130 HIS 0.002 0.001 HIS A 235 PHE 0.019 0.002 PHE A 566 TYR 0.018 0.002 TYR A 142 ARG 0.009 0.001 ARG A 234 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2055.81 seconds wall clock time: 36 minutes 32.27 seconds (2192.27 seconds total)