Starting phenix.real_space_refine on Fri Dec 27 09:03:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zqr_60389/12_2024/8zqr_60389.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zqr_60389/12_2024/8zqr_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8zqr_60389/12_2024/8zqr_60389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zqr_60389/12_2024/8zqr_60389.map" model { file = "/net/cci-nas-00/data/ceres_data/8zqr_60389/12_2024/8zqr_60389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zqr_60389/12_2024/8zqr_60389.cif" } resolution = 3.6 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= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 3.07, per 1000 atoms: 0.81 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: 1.07 Conformation dependent library (CDL) restraints added in 435.3 milliseconds 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: 0.35 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: 1.01 Time building geometry restraints manager: 1.24 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: 1.040 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.850 Find NCS groups from input model: 0.040 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.080 ------------------------------------------------------------------------------- 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 3885 Z= 0.307 Angle : 0.922 13.607 5306 Z= 0.524 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (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 TRP 0.034 0.002 TRP A 406 HIS 0.003 0.001 HIS A 221 PHE 0.014 0.001 PHE A 140 TYR 0.016 0.001 TYR A 67 ARG 0.002 0.000 ARG A 107 *********************** 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 : 0.395 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: 0.1408 time to fit residues: 14.1889 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 : 0.447 ------------------------------------------------------------------------------- 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 40 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3885 Z= 0.231 Angle : 0.729 9.551 5306 Z= 0.361 Chirality : 0.044 0.321 625 Planarity : 0.006 0.050 640 Dihedral : 9.837 65.222 583 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.09 % Allowed : 25.45 % Favored : 69.47 % 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: -0.18 (0.41), residues: 480 helix: 0.87 (0.31), residues: 327 sheet: None (None), residues: 0 loop : -2.33 (0.49), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 406 HIS 0.003 0.001 HIS A 162 PHE 0.011 0.001 PHE A 479 TYR 0.014 0.001 TYR A 439 ARG 0.002 0.000 ARG A 125 *********************** 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 99 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.562 Fit side-chains REVERT: A 62 TRP cc_start: 0.8399 (m100) cc_final: 0.8113 (m100) REVERT: A 73 GLU cc_start: 0.8300 (tt0) cc_final: 0.8031 (tt0) REVERT: A 284 MET cc_start: 0.7144 (tpp) cc_final: 0.6865 (tpt) REVERT: A 448 THR cc_start: 0.8236 (m) cc_final: 0.8010 (m) outliers start: 20 outliers final: 14 residues processed: 90 average time/residue: 0.1377 time to fit residues: 15.9560 Evaluate side-chains 83 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 309 ASP 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 24 optimal weight: 3.9990 chunk 13 optimal weight: 0.0570 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 0.0070 chunk 47 optimal weight: 4.9990 chunk 38 optimal weight: 0.0980 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3885 Z= 0.157 Angle : 0.636 9.448 5306 Z= 0.312 Chirality : 0.042 0.309 625 Planarity : 0.005 0.041 640 Dihedral : 6.848 54.784 582 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.58 % Allowed : 27.23 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.41), residues: 480 helix: 1.01 (0.31), residues: 335 sheet: None (None), residues: 0 loop : -1.85 (0.54), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 406 HIS 0.001 0.000 HIS A 221 PHE 0.011 0.001 PHE A 140 TYR 0.017 0.001 TYR A 496 ARG 0.001 0.000 ARG A 369 *********************** 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 102 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8284 (mp) REVERT: A 284 MET cc_start: 0.7111 (tpp) cc_final: 0.6865 (tpt) REVERT: A 318 MET cc_start: 0.6603 (mtt) cc_final: 0.6315 (mtt) REVERT: A 496 TYR cc_start: 0.6876 (t80) cc_final: 0.6239 (m-10) outliers start: 18 outliers final: 10 residues processed: 94 average time/residue: 0.1448 time to fit residues: 17.2604 Evaluate side-chains 82 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 347 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 43 optimal weight: 0.0030 chunk 46 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 26 optimal weight: 0.3980 chunk 0 optimal weight: 7.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3885 Z= 0.162 Angle : 0.646 9.594 5306 Z= 0.311 Chirality : 0.042 0.297 625 Planarity : 0.005 0.041 640 Dihedral : 6.102 54.725 582 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.33 % Allowed : 26.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.41), residues: 480 helix: 1.11 (0.30), residues: 335 sheet: None (None), residues: 0 loop : -1.76 (0.54), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 406 HIS 0.001 0.000 HIS A 209 PHE 0.011 0.001 PHE A 140 TYR 0.015 0.001 TYR A 364 ARG 0.002 0.000 ARG A 125 *********************** 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 88 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8236 (mp) REVERT: A 284 MET cc_start: 0.7133 (tpp) cc_final: 0.6740 (tpt) REVERT: A 496 TYR cc_start: 0.6956 (t80) cc_final: 0.6433 (m-10) outliers start: 17 outliers final: 10 residues processed: 82 average time/residue: 0.1409 time to fit residues: 14.7774 Evaluate side-chains 78 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 34 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3885 Z= 0.193 Angle : 0.635 9.584 5306 Z= 0.308 Chirality : 0.042 0.296 625 Planarity : 0.004 0.041 640 Dihedral : 5.932 54.677 582 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.83 % Allowed : 27.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.41), residues: 480 helix: 1.15 (0.30), residues: 334 sheet: None (None), residues: 0 loop : -1.70 (0.54), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 406 HIS 0.002 0.001 HIS A 209 PHE 0.010 0.001 PHE A 479 TYR 0.013 0.001 TYR A 364 ARG 0.002 0.000 ARG A 125 *********************** 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 94 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.370 Fit side-chains REVERT: A 97 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8222 (mp) REVERT: A 284 MET cc_start: 0.7167 (tpp) cc_final: 0.6803 (tpt) REVERT: A 411 ASP cc_start: 0.8055 (t0) cc_final: 0.7844 (t0) REVERT: A 496 TYR cc_start: 0.6988 (t80) cc_final: 0.6468 (m-10) outliers start: 19 outliers final: 14 residues processed: 88 average time/residue: 0.1349 time to fit residues: 15.1038 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 : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 129 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 4.9990 chunk 46 optimal weight: 0.1980 chunk 38 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 3885 Z= 0.160 Angle : 0.613 9.602 5306 Z= 0.296 Chirality : 0.041 0.294 625 Planarity : 0.004 0.041 640 Dihedral : 5.761 54.640 582 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.56 % Allowed : 28.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.41), residues: 480 helix: 1.28 (0.30), residues: 334 sheet: None (None), residues: 0 loop : -1.58 (0.55), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 406 HIS 0.001 0.000 HIS A 162 PHE 0.010 0.001 PHE A 140 TYR 0.013 0.001 TYR A 364 ARG 0.002 0.000 ARG A 125 *********************** 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 89 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.409 Fit side-chains REVERT: A 284 MET cc_start: 0.7136 (tpp) cc_final: 0.6784 (tpt) REVERT: A 411 ASP cc_start: 0.8009 (t0) cc_final: 0.7786 (t0) REVERT: A 496 TYR cc_start: 0.6994 (t80) cc_final: 0.6493 (m-10) outliers start: 14 outliers final: 12 residues processed: 81 average time/residue: 0.1249 time to fit residues: 13.2310 Evaluate side-chains 83 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 249 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 350 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 0.0570 chunk 8 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3885 Z= 0.169 Angle : 0.630 9.463 5306 Z= 0.301 Chirality : 0.042 0.287 625 Planarity : 0.004 0.040 640 Dihedral : 5.716 54.839 582 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.58 % Allowed : 29.52 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.41), residues: 480 helix: 1.32 (0.30), residues: 335 sheet: None (None), residues: 0 loop : -1.51 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 406 HIS 0.001 0.001 HIS A 209 PHE 0.010 0.001 PHE A 140 TYR 0.019 0.001 TYR A 364 ARG 0.002 0.000 ARG A 125 *********************** 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 90 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.405 Fit side-chains REVERT: A 177 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7197 (tp) REVERT: A 284 MET cc_start: 0.7108 (tpp) cc_final: 0.6775 (tpt) REVERT: A 411 ASP cc_start: 0.8073 (t0) cc_final: 0.7791 (t0) REVERT: A 496 TYR cc_start: 0.6986 (t80) cc_final: 0.6493 (m-10) outliers start: 18 outliers final: 14 residues processed: 82 average time/residue: 0.1280 time to fit residues: 13.6917 Evaluate side-chains 84 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 chunk 44 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 43 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3885 Z= 0.183 Angle : 0.657 14.341 5306 Z= 0.307 Chirality : 0.042 0.282 625 Planarity : 0.004 0.041 640 Dihedral : 5.712 54.684 582 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.33 % Allowed : 30.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.41), residues: 480 helix: 1.41 (0.30), residues: 329 sheet: None (None), residues: 0 loop : -1.57 (0.54), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 406 HIS 0.001 0.001 HIS A 162 PHE 0.009 0.001 PHE A 479 TYR 0.017 0.001 TYR A 364 ARG 0.002 0.000 ARG A 125 *********************** 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: 17 poor density : 70 time to evaluate : 0.383 Fit side-chains REVERT: A 177 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7145 (tp) REVERT: A 284 MET cc_start: 0.7125 (tpp) cc_final: 0.6788 (tpt) REVERT: A 411 ASP cc_start: 0.8121 (t0) cc_final: 0.7826 (t0) REVERT: A 496 TYR cc_start: 0.7026 (t80) cc_final: 0.6552 (m-10) outliers start: 17 outliers final: 12 residues processed: 80 average time/residue: 0.1264 time to fit residues: 13.2430 Evaluate side-chains 81 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 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 248 MET 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 13 optimal weight: 0.3980 chunk 38 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 chunk 42 optimal weight: 0.0770 chunk 28 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.0000 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 overall best weight: 0.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3885 Z= 0.153 Angle : 0.640 14.610 5306 Z= 0.300 Chirality : 0.041 0.279 625 Planarity : 0.004 0.041 640 Dihedral : 5.617 54.879 582 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.31 % Allowed : 30.79 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.42), residues: 480 helix: 1.51 (0.31), residues: 330 sheet: None (None), residues: 0 loop : -1.48 (0.54), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 406 HIS 0.001 0.000 HIS A 162 PHE 0.011 0.001 PHE A 140 TYR 0.020 0.001 TYR A 364 ARG 0.002 0.000 ARG A 125 *********************** 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 83 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.423 Fit side-chains REVERT: A 177 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7072 (tp) REVERT: A 284 MET cc_start: 0.7150 (tpp) cc_final: 0.6792 (tpt) REVERT: A 411 ASP cc_start: 0.8058 (t0) cc_final: 0.7846 (t0) REVERT: A 496 TYR cc_start: 0.6953 (t80) cc_final: 0.6492 (m-10) outliers start: 13 outliers final: 10 residues processed: 79 average time/residue: 0.1363 time to fit residues: 13.9429 Evaluate side-chains 76 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 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 177 LEU Chi-restraints excluded: chain A residue 221 HIS 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 44 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 23 optimal weight: 0.0470 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3885 Z= 0.171 Angle : 0.668 14.912 5306 Z= 0.308 Chirality : 0.041 0.281 625 Planarity : 0.004 0.039 640 Dihedral : 5.603 54.796 582 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.80 % Allowed : 31.30 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.42), residues: 480 helix: 1.49 (0.31), residues: 329 sheet: None (None), residues: 0 loop : -1.32 (0.56), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 406 HIS 0.002 0.001 HIS A 162 PHE 0.008 0.001 PHE A 479 TYR 0.018 0.001 TYR A 364 ARG 0.002 0.000 ARG A 125 ********************** 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: 11 poor density : 66 time to evaluate : 0.417 Fit side-chains REVERT: A 177 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6959 (tp) REVERT: A 284 MET cc_start: 0.7112 (tpp) cc_final: 0.6771 (tpt) REVERT: A 411 ASP cc_start: 0.8088 (t0) cc_final: 0.7779 (t0) REVERT: A 496 TYR cc_start: 0.7002 (t80) cc_final: 0.6506 (m-10) outliers start: 11 outliers final: 8 residues processed: 74 average time/residue: 0.1319 time to fit residues: 12.8553 Evaluate side-chains 73 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 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 177 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 38 optimal weight: 0.4980 chunk 15 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 7 optimal weight: 0.0570 chunk 33 optimal weight: 0.0070 chunk 2 optimal weight: 6.9990 chunk 27 optimal weight: 0.4980 chunk 43 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.3516 ------------------------------------------------------------------------------- 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 = 0.3790 r_free = 0.3790 target = 0.160214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.141763 restraints weight = 5869.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.144801 restraints weight = 3336.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.146843 restraints weight = 2262.144| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3885 Z= 0.156 Angle : 0.643 14.938 5306 Z= 0.301 Chirality : 0.041 0.281 625 Planarity : 0.004 0.040 640 Dihedral : 5.560 54.839 582 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.80 % Allowed : 31.81 % 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 (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: 1.06 (0.42), residues: 480 helix: 1.58 (0.30), residues: 329 sheet: None (None), residues: 0 loop : -1.28 (0.55), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 406 HIS 0.001 0.000 HIS A 162 PHE 0.011 0.001 PHE A 140 TYR 0.019 0.001 TYR A 364 ARG 0.002 0.000 ARG A 125 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1190.33 seconds wall clock time: 22 minutes 13.38 seconds (1333.38 seconds total)