Starting phenix.real_space_refine on Fri Aug 22 14:03:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zqr_60389/08_2025/8zqr_60389.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zqr_60389/08_2025/8zqr_60389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zqr_60389/08_2025/8zqr_60389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zqr_60389/08_2025/8zqr_60389.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zqr_60389/08_2025/8zqr_60389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zqr_60389/08_2025/8zqr_60389.map" } resolution = 3.6 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= 0.002 sd= 0.079 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 2524 2.51 5 N 564 2.21 5 O 670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3778 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3739 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 22, 'TRANS': 463} Chain breaks: 2 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.04, per 1000 atoms: 0.28 Number of scatterers: 3778 At special positions: 0 Unit cell: (83.3, 75.65, 94.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 670 8.00 N 564 7.00 C 2524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG B 1 " - " ASN A 301 " Time building additional restraints: 0.30 Conformation dependent library (CDL) restraints added in 117.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 884 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 1 sheets defined 73.7% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 4 through 21 removed outlier: 3.874A pdb=" N LEU A 8 " --> pdb=" O HIS A 4 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A 14 " --> pdb=" O ALA A 10 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU A 17 " --> pdb=" O VAL A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 63 removed outlier: 3.624A pdb=" N ALA A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR A 61 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TRP A 62 " --> pdb=" O MET A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 77 removed outlier: 4.332A pdb=" N ALA A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL A 75 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.576A pdb=" N TRP A 84 " --> pdb=" O GLY A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 102 removed outlier: 4.002A pdb=" N ILE A 96 " --> pdb=" O SER A 92 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 removed outlier: 3.502A pdb=" N ARG A 107 " --> pdb=" O ALA A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 122 removed outlier: 4.296A pdb=" N PHE A 118 " --> pdb=" O MET A 114 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE A 121 " --> pdb=" O PRO A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 130 removed outlier: 4.205A pdb=" N MET A 126 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY A 127 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 158 Processing helix chain 'A' and resid 160 through 179 removed outlier: 4.297A pdb=" N ILE A 166 " --> pdb=" O HIS A 162 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 208 removed outlier: 3.840A pdb=" N VAL A 190 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) Proline residue: A 204 - end of helix removed outlier: 3.668A pdb=" N SER A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 250 Processing helix chain 'A' and resid 254 through 264 removed outlier: 3.712A pdb=" N PHE A 258 " --> pdb=" O TRP A 254 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 264 " --> pdb=" O ARG A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 297 removed outlier: 3.838A pdb=" N ILE A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Proline residue: A 287 - end of helix Processing helix chain 'A' and resid 318 through 326 Processing helix chain 'A' and resid 329 through 346 removed outlier: 3.770A pdb=" N GLY A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 362 removed outlier: 4.493A pdb=" N SER A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 399 removed outlier: 3.520A pdb=" N VAL A 385 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 409 removed outlier: 3.532A pdb=" N LEU A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 417 Processing helix chain 'A' and resid 417 through 426 removed outlier: 3.854A pdb=" N CYS A 423 " --> pdb=" O PRO A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 450 removed outlier: 3.607A pdb=" N ALA A 435 " --> pdb=" O ASN A 431 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A 436 " --> pdb=" O THR A 432 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA A 437 " --> pdb=" O TYR A 433 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 502 removed outlier: 3.550A pdb=" N ILE A 492 " --> pdb=" O PHE A 488 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N CYS A 493 " --> pdb=" O LEU A 489 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 466 through 467 220 hydrogen bonds defined for protein. 654 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: 0.64 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 564 1.30 - 1.43: 1102 1.43 - 1.56: 2184 1.56 - 1.68: 0 1.68 - 1.81: 35 Bond restraints: 3885 Sorted by residual: bond pdb=" N ILE A 68 " pdb=" CA ILE A 68 " ideal model delta sigma weight residual 1.459 1.388 0.071 1.25e-02 6.40e+03 3.25e+01 bond pdb=" CA VAL A 63 " pdb=" C VAL A 63 " ideal model delta sigma weight residual 1.523 1.463 0.060 1.27e-02 6.20e+03 2.22e+01 bond pdb=" CA GLY A 65 " pdb=" C GLY A 65 " ideal model delta sigma weight residual 1.514 1.451 0.064 1.41e-02 5.03e+03 2.04e+01 bond pdb=" CA VAL A 63 " pdb=" CB VAL A 63 " ideal model delta sigma weight residual 1.540 1.480 0.060 1.36e-02 5.41e+03 1.94e+01 bond pdb=" C VAL A 63 " pdb=" O VAL A 63 " ideal model delta sigma weight residual 1.236 1.184 0.052 1.19e-02 7.06e+03 1.93e+01 ... (remaining 3880 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 5192 2.72 - 5.44: 89 5.44 - 8.16: 22 8.16 - 10.89: 2 10.89 - 13.61: 1 Bond angle restraints: 5306 Sorted by residual: angle pdb=" C ASN A 69 " pdb=" CA ASN A 69 " pdb=" CB ASN A 69 " ideal model delta sigma weight residual 109.34 120.14 -10.80 1.55e+00 4.16e-01 4.86e+01 angle pdb=" N ILE A 68 " pdb=" CA ILE A 68 " pdb=" C ILE A 68 " ideal model delta sigma weight residual 109.34 122.95 -13.61 2.08e+00 2.31e-01 4.28e+01 angle pdb=" N GLY A 70 " pdb=" CA GLY A 70 " pdb=" C GLY A 70 " ideal model delta sigma weight residual 112.77 120.83 -8.06 1.28e+00 6.10e-01 3.97e+01 angle pdb=" N ASP A 317 " pdb=" CA ASP A 317 " pdb=" C ASP A 317 " ideal model delta sigma weight residual 113.38 107.46 5.92 1.23e+00 6.61e-01 2.32e+01 angle pdb=" O GLY A 66 " pdb=" C GLY A 66 " pdb=" N TYR A 67 " ideal model delta sigma weight residual 122.70 128.75 -6.05 1.30e+00 5.92e-01 2.17e+01 ... (remaining 5301 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.90: 1992 21.90 - 43.79: 205 43.79 - 65.68: 30 65.68 - 87.58: 11 87.58 - 109.47: 4 Dihedral angle restraints: 2242 sinusoidal: 845 harmonic: 1397 Sorted by residual: dihedral pdb=" C ILE A 68 " pdb=" N ILE A 68 " pdb=" CA ILE A 68 " pdb=" CB ILE A 68 " ideal model delta harmonic sigma weight residual -122.00 -136.16 14.16 0 2.50e+00 1.60e-01 3.21e+01 dihedral pdb=" CA GLU A 376 " pdb=" C GLU A 376 " pdb=" N ILE A 377 " pdb=" CA ILE A 377 " ideal model delta harmonic sigma weight residual -180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA LYS A 375 " pdb=" C LYS A 375 " pdb=" N GLU A 376 " pdb=" CA GLU A 376 " ideal model delta harmonic sigma weight residual 180.00 -156.95 -23.05 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 2239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 613 0.136 - 0.273: 7 0.273 - 0.409: 1 0.409 - 0.545: 3 0.545 - 0.682: 1 Chirality restraints: 625 Sorted by residual: chirality pdb=" CA ILE A 68 " pdb=" N ILE A 68 " pdb=" C ILE A 68 " pdb=" CB ILE A 68 " both_signs ideal model delta sigma weight residual False 2.43 1.75 0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" CB VAL A 63 " pdb=" CA VAL A 63 " pdb=" CG1 VAL A 63 " pdb=" CG2 VAL A 63 " both_signs ideal model delta sigma weight residual False -2.63 -2.16 -0.47 2.00e-01 2.50e+01 5.61e+00 chirality pdb=" CA VAL A 63 " pdb=" N VAL A 63 " pdb=" C VAL A 63 " pdb=" CB VAL A 63 " both_signs ideal model delta sigma weight residual False 2.44 1.98 0.46 2.00e-01 2.50e+01 5.30e+00 ... (remaining 622 not shown) Planarity restraints: 641 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 66 " -0.013 2.00e-02 2.50e+03 2.88e-02 8.30e+00 pdb=" C GLY A 66 " 0.050 2.00e-02 2.50e+03 pdb=" O GLY A 66 " -0.019 2.00e-02 2.50e+03 pdb=" N TYR A 67 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 203 " -0.037 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO A 204 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 204 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 204 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 406 " 0.018 2.00e-02 2.50e+03 1.31e-02 4.28e+00 pdb=" CG TRP A 406 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A 406 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 406 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 406 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 406 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 406 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 406 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 406 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 406 " 0.009 2.00e-02 2.50e+03 ... (remaining 638 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 736 2.76 - 3.30: 3602 3.30 - 3.83: 5919 3.83 - 4.37: 6563 4.37 - 4.90: 11532 Nonbonded interactions: 28352 Sorted by model distance: nonbonded pdb=" O ILE A 294 " pdb=" OG1 THR A 298 " model vdw 2.229 3.040 nonbonded pdb=" OG1 THR A 113 " pdb=" OE1 GLN A 255 " model vdw 2.298 3.040 nonbonded pdb=" N ASP A 512 " pdb=" OD1 ASP A 512 " model vdw 2.374 3.120 nonbonded pdb=" OH TYR A 433 " pdb=" O PHE A 514 " model vdw 2.400 3.040 nonbonded pdb=" OG1 THR A 303 " pdb=" N ALA A 304 " model vdw 2.427 3.120 ... (remaining 28347 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: 1.490 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.700 Find NCS groups from input model: 0.020 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:1.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 3888 Z= 0.301 Angle : 0.945 13.607 5315 Z= 0.528 Chirality : 0.064 0.682 625 Planarity : 0.006 0.056 640 Dihedral : 18.433 109.470 1358 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.76 % Allowed : 26.72 % Favored : 72.52 % Cbeta Deviations : 0.45 % 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 aren not related in a simple way. whole: -0.86 (0.39), residues: 480 helix: 0.31 (0.31), residues: 314 sheet: None (None), residues: 0 loop : -2.28 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 107 TYR 0.016 0.001 TYR A 67 PHE 0.014 0.001 PHE A 140 TRP 0.034 0.002 TRP A 406 HIS 0.003 0.001 HIS A 221 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 3885) covalent geometry : angle 0.92212 ( 5306) hydrogen bonds : bond 0.22483 ( 220) hydrogen bonds : angle 6.59944 ( 654) link_BETA1-4 : bond 0.00672 ( 2) link_BETA1-4 : angle 3.97131 ( 6) link_NAG-ASN : bond 0.01319 ( 1) link_NAG-ASN : angle 6.76227 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 time to evaluate : 0.135 Fit side-chains REVERT: A 73 GLU cc_start: 0.8223 (tt0) cc_final: 0.7654 (tt0) REVERT: A 371 ASN cc_start: 0.7652 (p0) cc_final: 0.7186 (m110) outliers start: 3 outliers final: 2 residues processed: 79 average time/residue: 0.0664 time to fit residues: 6.7036 Evaluate side-chains 75 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 432 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.154804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.135670 restraints weight = 6022.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.138636 restraints weight = 3392.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.140658 restraints weight = 2305.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.141989 restraints weight = 1785.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.142939 restraints weight = 1495.186| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3888 Z= 0.146 Angle : 0.746 9.594 5315 Z= 0.360 Chirality : 0.044 0.323 625 Planarity : 0.005 0.049 640 Dihedral : 9.375 59.973 583 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 5.09 % Allowed : 25.19 % Favored : 69.72 % 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 aren not related in a simple way. whole: -0.13 (0.41), residues: 480 helix: 0.88 (0.31), residues: 328 sheet: None (None), residues: 0 loop : -2.26 (0.50), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 260 TYR 0.013 0.001 TYR A 439 PHE 0.011 0.001 PHE A 418 TRP 0.029 0.001 TRP A 406 HIS 0.002 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 3885) covalent geometry : angle 0.71960 ( 5306) hydrogen bonds : bond 0.05327 ( 220) hydrogen bonds : angle 4.77378 ( 654) link_BETA1-4 : bond 0.00665 ( 2) link_BETA1-4 : angle 3.96224 ( 6) link_NAG-ASN : bond 0.01249 ( 1) link_NAG-ASN : angle 6.26615 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.148 Fit side-chains REVERT: A 62 TRP cc_start: 0.8474 (m100) cc_final: 0.8200 (m100) REVERT: A 73 GLU cc_start: 0.8514 (tt0) cc_final: 0.8130 (tt0) REVERT: A 284 MET cc_start: 0.7490 (tpp) cc_final: 0.7245 (tpt) outliers start: 20 outliers final: 13 residues processed: 91 average time/residue: 0.0560 time to fit residues: 6.6393 Evaluate side-chains 83 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 350 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.156135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.137349 restraints weight = 5867.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.140374 restraints weight = 3306.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.142374 restraints weight = 2244.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.143728 restraints weight = 1732.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.144536 restraints weight = 1448.312| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3888 Z= 0.131 Angle : 0.682 9.474 5315 Z= 0.326 Chirality : 0.043 0.306 625 Planarity : 0.005 0.042 640 Dihedral : 6.761 54.721 582 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.09 % Allowed : 26.21 % Favored : 68.70 % 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 aren not related in a simple way. whole: 0.13 (0.41), residues: 480 helix: 0.96 (0.31), residues: 333 sheet: None (None), residues: 0 loop : -1.94 (0.53), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 125 TYR 0.017 0.001 TYR A 496 PHE 0.011 0.001 PHE A 140 TRP 0.029 0.001 TRP A 406 HIS 0.002 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 3885) covalent geometry : angle 0.65517 ( 5306) hydrogen bonds : bond 0.04569 ( 220) hydrogen bonds : angle 4.45249 ( 654) link_BETA1-4 : bond 0.00601 ( 2) link_BETA1-4 : angle 3.83837 ( 6) link_NAG-ASN : bond 0.01176 ( 1) link_NAG-ASN : angle 5.99260 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.181 Fit side-chains REVERT: A 73 GLU cc_start: 0.8421 (tt0) cc_final: 0.8216 (tt0) REVERT: A 97 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8174 (mp) REVERT: A 120 GLN cc_start: 0.6914 (mt0) cc_final: 0.6530 (mp10) REVERT: A 284 MET cc_start: 0.7491 (tpp) cc_final: 0.7266 (tpt) REVERT: A 496 TYR cc_start: 0.7175 (t80) cc_final: 0.6152 (m-10) outliers start: 20 outliers final: 11 residues processed: 95 average time/residue: 0.0523 time to fit residues: 6.4033 Evaluate side-chains 80 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 347 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 42 optimal weight: 0.0170 chunk 37 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 0.0040 chunk 34 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.4830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.158161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.139537 restraints weight = 5867.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.142622 restraints weight = 3274.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.144524 restraints weight = 2204.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.145955 restraints weight = 1705.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.146841 restraints weight = 1423.071| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3888 Z= 0.117 Angle : 0.679 9.595 5315 Z= 0.319 Chirality : 0.042 0.298 625 Planarity : 0.005 0.041 640 Dihedral : 6.180 54.578 582 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.07 % Allowed : 28.24 % Favored : 67.68 % 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 aren not related in a simple way. whole: 0.35 (0.41), residues: 480 helix: 1.10 (0.31), residues: 334 sheet: None (None), residues: 0 loop : -1.80 (0.54), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 125 TYR 0.014 0.001 TYR A 364 PHE 0.011 0.001 PHE A 140 TRP 0.029 0.001 TRP A 406 HIS 0.001 0.000 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 3885) covalent geometry : angle 0.65316 ( 5306) hydrogen bonds : bond 0.03947 ( 220) hydrogen bonds : angle 4.36476 ( 654) link_BETA1-4 : bond 0.00626 ( 2) link_BETA1-4 : angle 3.73805 ( 6) link_NAG-ASN : bond 0.01182 ( 1) link_NAG-ASN : angle 5.89843 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.158 Fit side-chains REVERT: A 97 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8104 (mp) REVERT: A 284 MET cc_start: 0.7538 (tpp) cc_final: 0.7122 (tpt) REVERT: A 411 ASP cc_start: 0.8050 (t0) cc_final: 0.7806 (t0) REVERT: A 496 TYR cc_start: 0.7199 (t80) cc_final: 0.6273 (m-10) outliers start: 16 outliers final: 10 residues processed: 84 average time/residue: 0.0582 time to fit residues: 6.3398 Evaluate side-chains 80 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 412 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 20 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 39 optimal weight: 0.1980 chunk 14 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.157750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.138936 restraints weight = 5845.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.141938 restraints weight = 3280.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.143973 restraints weight = 2220.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.145233 restraints weight = 1707.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.146209 restraints weight = 1438.733| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3888 Z= 0.118 Angle : 0.644 9.599 5315 Z= 0.305 Chirality : 0.042 0.295 625 Planarity : 0.004 0.041 640 Dihedral : 5.906 54.747 582 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.07 % Allowed : 28.75 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.42), residues: 480 helix: 1.17 (0.31), residues: 333 sheet: None (None), residues: 0 loop : -1.59 (0.55), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 125 TYR 0.014 0.001 TYR A 364 PHE 0.010 0.001 PHE A 140 TRP 0.027 0.001 TRP A 406 HIS 0.001 0.000 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 3885) covalent geometry : angle 0.61807 ( 5306) hydrogen bonds : bond 0.03813 ( 220) hydrogen bonds : angle 4.29103 ( 654) link_BETA1-4 : bond 0.00666 ( 2) link_BETA1-4 : angle 3.57236 ( 6) link_NAG-ASN : bond 0.01164 ( 1) link_NAG-ASN : angle 5.77528 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.147 Fit side-chains REVERT: A 97 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8090 (mp) REVERT: A 284 MET cc_start: 0.7529 (tpp) cc_final: 0.7148 (tpt) REVERT: A 411 ASP cc_start: 0.8091 (t0) cc_final: 0.7851 (t0) REVERT: A 496 TYR cc_start: 0.7233 (t80) cc_final: 0.6305 (m-10) outliers start: 16 outliers final: 11 residues processed: 84 average time/residue: 0.0467 time to fit residues: 5.2365 Evaluate side-chains 81 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 412 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3730 r_free = 0.3730 target = 0.154992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.136578 restraints weight = 5908.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.139484 restraints weight = 3419.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.141494 restraints weight = 2344.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.142863 restraints weight = 1806.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.143736 restraints weight = 1507.040| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3888 Z= 0.126 Angle : 0.653 9.575 5315 Z= 0.310 Chirality : 0.042 0.294 625 Planarity : 0.004 0.041 640 Dihedral : 5.822 54.528 582 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.33 % Allowed : 28.50 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.41), residues: 480 helix: 1.17 (0.30), residues: 335 sheet: None (None), residues: 0 loop : -1.76 (0.54), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 125 TYR 0.011 0.001 TYR A 364 PHE 0.010 0.001 PHE A 479 TRP 0.023 0.001 TRP A 406 HIS 0.002 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 3885) covalent geometry : angle 0.62892 ( 5306) hydrogen bonds : bond 0.04007 ( 220) hydrogen bonds : angle 4.26017 ( 654) link_BETA1-4 : bond 0.00701 ( 2) link_BETA1-4 : angle 3.50903 ( 6) link_NAG-ASN : bond 0.01133 ( 1) link_NAG-ASN : angle 5.60406 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.148 Fit side-chains REVERT: A 97 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8070 (mp) REVERT: A 177 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7124 (tp) REVERT: A 284 MET cc_start: 0.7521 (tpp) cc_final: 0.7133 (tpt) REVERT: A 411 ASP cc_start: 0.8121 (t0) cc_final: 0.7902 (t0) REVERT: A 496 TYR cc_start: 0.7269 (t80) cc_final: 0.6313 (m-10) outliers start: 17 outliers final: 13 residues processed: 84 average time/residue: 0.0620 time to fit residues: 6.7166 Evaluate side-chains 86 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 412 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.155513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.137100 restraints weight = 6045.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.140093 restraints weight = 3447.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.142087 restraints weight = 2340.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.143480 restraints weight = 1798.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.144410 restraints weight = 1492.722| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3888 Z= 0.121 Angle : 0.641 9.583 5315 Z= 0.306 Chirality : 0.041 0.293 625 Planarity : 0.004 0.040 640 Dihedral : 5.808 54.518 582 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.83 % Allowed : 28.50 % Favored : 66.67 % 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 aren not related in a simple way. whole: 0.58 (0.41), residues: 480 helix: 1.24 (0.30), residues: 334 sheet: None (None), residues: 0 loop : -1.62 (0.54), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 125 TYR 0.019 0.001 TYR A 364 PHE 0.009 0.001 PHE A 140 TRP 0.024 0.001 TRP A 406 HIS 0.001 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 3885) covalent geometry : angle 0.61663 ( 5306) hydrogen bonds : bond 0.03813 ( 220) hydrogen bonds : angle 4.23104 ( 654) link_BETA1-4 : bond 0.00665 ( 2) link_BETA1-4 : angle 3.48789 ( 6) link_NAG-ASN : bond 0.01122 ( 1) link_NAG-ASN : angle 5.56184 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.112 Fit side-chains REVERT: A 73 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7922 (tp30) REVERT: A 97 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8021 (mp) REVERT: A 177 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7105 (tp) REVERT: A 284 MET cc_start: 0.7528 (tpp) cc_final: 0.7135 (tpt) REVERT: A 411 ASP cc_start: 0.8074 (t0) cc_final: 0.7866 (t0) REVERT: A 496 TYR cc_start: 0.7298 (t80) cc_final: 0.6341 (m-10) outliers start: 19 outliers final: 12 residues processed: 86 average time/residue: 0.0575 time to fit residues: 6.3301 Evaluate side-chains 85 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 412 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 17 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 23 optimal weight: 0.0870 chunk 21 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 5 optimal weight: 0.0070 chunk 25 optimal weight: 1.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.156628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.138254 restraints weight = 5900.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.141133 restraints weight = 3338.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.143278 restraints weight = 2275.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.144543 restraints weight = 1739.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.145535 restraints weight = 1453.131| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3888 Z= 0.111 Angle : 0.633 9.600 5315 Z= 0.299 Chirality : 0.041 0.290 625 Planarity : 0.004 0.040 640 Dihedral : 5.690 54.613 582 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.58 % Allowed : 29.26 % Favored : 66.16 % 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 aren not related in a simple way. whole: 0.75 (0.41), residues: 480 helix: 1.32 (0.30), residues: 335 sheet: None (None), residues: 0 loop : -1.47 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 125 TYR 0.018 0.001 TYR A 364 PHE 0.010 0.001 PHE A 140 TRP 0.023 0.001 TRP A 406 HIS 0.002 0.000 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 3885) covalent geometry : angle 0.60884 ( 5306) hydrogen bonds : bond 0.03494 ( 220) hydrogen bonds : angle 4.12561 ( 654) link_BETA1-4 : bond 0.00694 ( 2) link_BETA1-4 : angle 3.42131 ( 6) link_NAG-ASN : bond 0.01137 ( 1) link_NAG-ASN : angle 5.50567 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.138 Fit side-chains REVERT: A 97 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8072 (mp) REVERT: A 177 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.6996 (tp) REVERT: A 284 MET cc_start: 0.7543 (tpp) cc_final: 0.7162 (tpt) REVERT: A 496 TYR cc_start: 0.7303 (t80) cc_final: 0.6376 (m-10) outliers start: 18 outliers final: 13 residues processed: 79 average time/residue: 0.0584 time to fit residues: 5.9510 Evaluate side-chains 78 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 412 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.158127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.139590 restraints weight = 5990.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.142623 restraints weight = 3399.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.144654 restraints weight = 2306.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.146026 restraints weight = 1772.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.146855 restraints weight = 1483.030| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3888 Z= 0.118 Angle : 0.645 9.509 5315 Z= 0.305 Chirality : 0.041 0.273 625 Planarity : 0.004 0.039 640 Dihedral : 5.665 54.646 582 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.82 % Allowed : 30.79 % Favored : 65.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.41), residues: 480 helix: 1.44 (0.30), residues: 329 sheet: None (None), residues: 0 loop : -1.60 (0.53), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 125 TYR 0.018 0.001 TYR A 364 PHE 0.009 0.001 PHE A 140 TRP 0.017 0.001 TRP A 406 HIS 0.001 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 3885) covalent geometry : angle 0.62185 ( 5306) hydrogen bonds : bond 0.03645 ( 220) hydrogen bonds : angle 4.13867 ( 654) link_BETA1-4 : bond 0.00725 ( 2) link_BETA1-4 : angle 3.38517 ( 6) link_NAG-ASN : bond 0.01044 ( 1) link_NAG-ASN : angle 5.47734 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.136 Fit side-chains REVERT: A 97 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8058 (mp) REVERT: A 177 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.6998 (tp) REVERT: A 284 MET cc_start: 0.7505 (tpp) cc_final: 0.7119 (tpt) REVERT: A 496 TYR cc_start: 0.7321 (t80) cc_final: 0.6403 (m-10) outliers start: 15 outliers final: 12 residues processed: 74 average time/residue: 0.0638 time to fit residues: 6.0775 Evaluate side-chains 77 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 412 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 chunk 18 optimal weight: 0.0870 chunk 42 optimal weight: 0.0670 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.4496 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.158773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.140399 restraints weight = 6001.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.143370 restraints weight = 3390.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.145413 restraints weight = 2299.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.146679 restraints weight = 1768.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.147633 restraints weight = 1483.925| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3888 Z= 0.114 Angle : 0.641 9.546 5315 Z= 0.307 Chirality : 0.041 0.274 625 Planarity : 0.004 0.039 640 Dihedral : 5.605 54.744 582 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.56 % Allowed : 31.04 % Favored : 65.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.41), residues: 480 helix: 1.44 (0.30), residues: 331 sheet: None (None), residues: 0 loop : -1.52 (0.55), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 125 TYR 0.017 0.001 TYR A 364 PHE 0.010 0.001 PHE A 140 TRP 0.019 0.001 TRP A 406 HIS 0.002 0.000 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 3885) covalent geometry : angle 0.61826 ( 5306) hydrogen bonds : bond 0.03404 ( 220) hydrogen bonds : angle 4.05499 ( 654) link_BETA1-4 : bond 0.00708 ( 2) link_BETA1-4 : angle 3.36213 ( 6) link_NAG-ASN : bond 0.01141 ( 1) link_NAG-ASN : angle 5.47767 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.115 Fit side-chains REVERT: A 97 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8055 (mp) REVERT: A 177 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7019 (tp) REVERT: A 284 MET cc_start: 0.7526 (tpp) cc_final: 0.7146 (tpt) REVERT: A 496 TYR cc_start: 0.7253 (t80) cc_final: 0.6314 (m-10) outliers start: 14 outliers final: 9 residues processed: 71 average time/residue: 0.0536 time to fit residues: 5.0573 Evaluate side-chains 71 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 412 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 15 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 46 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 47 optimal weight: 0.0030 chunk 43 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.156740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.138732 restraints weight = 5861.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.141742 restraints weight = 3297.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.143756 restraints weight = 2220.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.145129 restraints weight = 1695.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.145936 restraints weight = 1407.667| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3888 Z= 0.119 Angle : 0.643 9.587 5315 Z= 0.307 Chirality : 0.042 0.277 625 Planarity : 0.004 0.039 640 Dihedral : 5.606 54.771 582 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.05 % Allowed : 31.30 % Favored : 65.65 % 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 aren not related in a simple way. whole: 0.92 (0.41), residues: 480 helix: 1.50 (0.30), residues: 329 sheet: None (None), residues: 0 loop : -1.41 (0.55), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 125 TYR 0.017 0.001 TYR A 364 PHE 0.011 0.001 PHE A 258 TRP 0.018 0.001 TRP A 406 HIS 0.001 0.000 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 3885) covalent geometry : angle 0.62008 ( 5306) hydrogen bonds : bond 0.03578 ( 220) hydrogen bonds : angle 4.09011 ( 654) link_BETA1-4 : bond 0.00758 ( 2) link_BETA1-4 : angle 3.32838 ( 6) link_NAG-ASN : bond 0.01131 ( 1) link_NAG-ASN : angle 5.48619 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 862.48 seconds wall clock time: 15 minutes 30.79 seconds (930.79 seconds total)