Starting phenix.real_space_refine on Fri Mar 14 04:47:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xck_33123/03_2025/7xck_33123.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xck_33123/03_2025/7xck_33123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xck_33123/03_2025/7xck_33123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xck_33123/03_2025/7xck_33123.map" model { file = "/net/cci-nas-00/data/ceres_data/7xck_33123/03_2025/7xck_33123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xck_33123/03_2025/7xck_33123.cif" } resolution = 2.5 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= -0.001 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4868 atoms to isotropic. 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 21 5.16 5 C 3473 2.51 5 N 927 2.21 5 O 1067 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5488 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1688 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 210} Chain breaks: 1 Chain: "B" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1615 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 200} Chain: "M" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2147 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 16, 'TRANS': 252} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: 5.60, per 1000 atoms: 1.02 Number of scatterers: 5488 At special positions: 0 Unit cell: (113.9, 61.64, 122.61, 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 21 16.00 O 1067 8.00 N 927 7.00 C 3473 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 210 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.04 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS M 336 " - pdb=" SG CYS M 361 " distance=2.03 Simple disulfide: pdb=" SG CYS M 379 " - pdb=" SG CYS M 432 " distance=2.04 Simple disulfide: pdb=" SG CYS M 480 " - pdb=" SG CYS M 488 " distance=2.03 Simple disulfide: pdb=" SG CYS M 538 " - pdb=" SG CYS M 590 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " BETA1-6 " NAG C 1 " - " FUC C 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG C 1 " - " ASN M 343 " Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 794.1 milliseconds 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1302 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 14 sheets defined 9.7% alpha, 38.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.646A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.942A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 80 through 84 removed outlier: 4.031A pdb=" N PHE B 84 " --> pdb=" O PRO B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 188 removed outlier: 3.542A pdb=" N LYS B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) Processing helix chain 'M' and resid 338 through 343 Processing helix chain 'M' and resid 365 through 369 Processing helix chain 'M' and resid 383 through 390 removed outlier: 3.529A pdb=" N LEU M 387 " --> pdb=" O PRO M 384 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASN M 388 " --> pdb=" O THR M 385 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU M 390 " --> pdb=" O LEU M 387 " (cutoff:3.500A) Processing helix chain 'M' and resid 403 through 410 removed outlier: 3.521A pdb=" N GLU M 406 " --> pdb=" O ARG M 403 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL M 407 " --> pdb=" O GLY M 404 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG M 408 " --> pdb=" O ASP M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 422 Processing helix chain 'M' and resid 438 through 443 removed outlier: 3.707A pdb=" N SER M 443 " --> pdb=" O ASN M 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.515A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TRP A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE A 34 " --> pdb=" O TRP A 50 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASN A 116 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.515A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TRP A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE A 34 " --> pdb=" O TRP A 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 138 removed outlier: 6.127A pdb=" N TYR A 190 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 134 through 138 removed outlier: 6.127A pdb=" N TYR A 190 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 165 through 168 Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.402A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N TYR B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.402A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 116 through 118 removed outlier: 3.957A pdb=" N VAL B 133 " --> pdb=" O PHE B 118 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN B 138 " --> pdb=" O TYR B 173 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR B 173 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 145 through 149 Processing sheet with id=AB3, first strand: chain 'M' and resid 325 through 328 removed outlier: 5.842A pdb=" N ASP M 574 " --> pdb=" O ILE M 587 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY M 566 " --> pdb=" O ASP M 574 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 354 through 358 Processing sheet with id=AB5, first strand: chain 'M' and resid 452 through 454 209 hydrogen bonds defined for protein. 513 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: 1.82 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 948 1.32 - 1.45: 1605 1.45 - 1.58: 3044 1.58 - 1.71: 0 1.71 - 1.84: 24 Bond restraints: 5621 Sorted by residual: bond pdb=" C ALA M 344 " pdb=" N THR M 345 " ideal model delta sigma weight residual 1.335 1.278 0.057 1.25e-02 6.40e+03 2.05e+01 bond pdb=" CA ALA M 344 " pdb=" CB ALA M 344 " ideal model delta sigma weight residual 1.528 1.474 0.054 1.58e-02 4.01e+03 1.15e+01 bond pdb=" C ALA M 344 " pdb=" O ALA M 344 " ideal model delta sigma weight residual 1.235 1.201 0.034 1.20e-02 6.94e+03 8.18e+00 bond pdb=" C ASN M 343 " pdb=" O ASN M 343 " ideal model delta sigma weight residual 1.235 1.197 0.038 1.32e-02 5.74e+03 8.17e+00 bond pdb=" CA ALA M 344 " pdb=" C ALA M 344 " ideal model delta sigma weight residual 1.524 1.486 0.038 1.33e-02 5.65e+03 8.00e+00 ... (remaining 5616 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 7496 2.21 - 4.43: 120 4.43 - 6.64: 25 6.64 - 8.85: 2 8.85 - 11.07: 1 Bond angle restraints: 7644 Sorted by residual: angle pdb=" CA ASN M 334 " pdb=" C ASN M 334 " pdb=" O ASN M 334 " ideal model delta sigma weight residual 121.15 116.26 4.89 1.10e+00 8.26e-01 1.98e+01 angle pdb=" C VAL B 150 " pdb=" N ASP B 151 " pdb=" CA ASP B 151 " ideal model delta sigma weight residual 121.54 129.19 -7.65 1.91e+00 2.74e-01 1.60e+01 angle pdb=" C ASN M 343 " pdb=" CA ASN M 343 " pdb=" CB ASN M 343 " ideal model delta sigma weight residual 111.02 104.60 6.42 1.61e+00 3.86e-01 1.59e+01 angle pdb=" C PRO A 161 " pdb=" N GLU A 162 " pdb=" CA GLU A 162 " ideal model delta sigma weight residual 120.26 125.14 -4.88 1.34e+00 5.57e-01 1.33e+01 angle pdb=" C SER B 95 " pdb=" CA SER B 95 " pdb=" CB SER B 95 " ideal model delta sigma weight residual 115.89 111.20 4.69 1.32e+00 5.74e-01 1.26e+01 ... (remaining 7639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 3108 17.59 - 35.17: 228 35.17 - 52.76: 47 52.76 - 70.34: 5 70.34 - 87.93: 4 Dihedral angle restraints: 3392 sinusoidal: 1356 harmonic: 2036 Sorted by residual: dihedral pdb=" CB CYS A 154 " pdb=" SG CYS A 154 " pdb=" SG CYS A 210 " pdb=" CB CYS A 210 " ideal model delta sinusoidal sigma weight residual 93.00 162.64 -69.64 1 1.00e+01 1.00e-02 6.26e+01 dihedral pdb=" CB CYS M 538 " pdb=" SG CYS M 538 " pdb=" SG CYS M 590 " pdb=" CB CYS M 590 " ideal model delta sinusoidal sigma weight residual -86.00 -38.35 -47.65 1 1.00e+01 1.00e-02 3.13e+01 dihedral pdb=" CB CYS M 379 " pdb=" SG CYS M 379 " pdb=" SG CYS M 432 " pdb=" CB CYS M 432 " ideal model delta sinusoidal sigma weight residual -86.00 -51.56 -34.44 1 1.00e+01 1.00e-02 1.68e+01 ... (remaining 3389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 855 0.142 - 0.284: 2 0.284 - 0.425: 0 0.425 - 0.567: 0 0.567 - 0.709: 1 Chirality restraints: 858 Sorted by residual: chirality pdb=" C1 FUC C 3 " pdb=" O6 NAG C 1 " pdb=" C2 FUC C 3 " pdb=" O5 FUC C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.19e+01 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN M 343 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" CA VAL A 37 " pdb=" N VAL A 37 " pdb=" C VAL A 37 " pdb=" CB VAL A 37 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.69e-01 ... (remaining 855 not shown) Planarity restraints: 982 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " -0.045 2.00e-02 2.50e+03 3.72e-02 1.73e+01 pdb=" C7 NAG C 1 " 0.011 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " -0.034 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " 0.060 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 2 " 0.041 2.00e-02 2.50e+03 3.36e-02 1.41e+01 pdb=" C7 NAG C 2 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG C 2 " 0.032 2.00e-02 2.50e+03 pdb=" N2 NAG C 2 " -0.052 2.00e-02 2.50e+03 pdb=" O7 NAG C 2 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA M 520 " 0.043 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO M 521 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO M 521 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO M 521 " 0.036 5.00e-02 4.00e+02 ... (remaining 979 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 246 2.72 - 3.27: 5007 3.27 - 3.81: 8362 3.81 - 4.36: 10652 4.36 - 4.90: 18600 Nonbonded interactions: 42867 Sorted by model distance: nonbonded pdb=" OH TYR M 369 " pdb=" O PRO M 384 " model vdw 2.179 3.040 nonbonded pdb=" OG SER B 64 " pdb=" OG1 THR B 75 " model vdw 2.198 3.040 nonbonded pdb=" OG1 THR A 149 " pdb=" O VAL A 198 " model vdw 2.228 3.040 nonbonded pdb=" OE1 GLU B 105 " pdb=" OH TYR B 173 " model vdw 2.296 3.040 nonbonded pdb=" O ASP M 442 " pdb=" ND2 ASN M 448 " model vdw 2.307 3.120 ... (remaining 42862 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 individual isotropic 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: 8.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.990 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 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 : 0.004 0.057 5621 Z= 0.251 Angle : 0.713 11.067 7644 Z= 0.389 Chirality : 0.052 0.709 858 Planarity : 0.006 0.065 981 Dihedral : 12.630 87.930 2066 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.60 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.89 (0.32), residues: 696 helix: -3.99 (0.85), residues: 20 sheet: 0.21 (0.33), residues: 271 loop : -0.98 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 436 HIS 0.004 0.001 HIS M 519 PHE 0.012 0.001 PHE M 374 TYR 0.007 0.001 TYR A 159 ARG 0.002 0.000 ARG M 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.550 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 1.3785 time to fit residues: 99.0879 Evaluate side-chains 57 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 17 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 0.0060 chunk 20 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 GLN B 189 HIS M 417 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.183246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.118141 restraints weight = 6045.314| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.52 r_work: 0.3278 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.0816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5621 Z= 0.186 Angle : 0.590 8.922 7644 Z= 0.305 Chirality : 0.046 0.138 858 Planarity : 0.005 0.060 981 Dihedral : 4.951 20.273 823 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.47 % Allowed : 5.92 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.84 (0.33), residues: 696 helix: -4.43 (0.54), residues: 26 sheet: 0.37 (0.33), residues: 268 loop : -0.94 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 47 HIS 0.004 0.001 HIS B 92 PHE 0.012 0.001 PHE M 377 TYR 0.008 0.001 TYR M 369 ARG 0.004 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 43 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7308 (mp10) REVERT: A 82 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7646 (tp30) REVERT: B 117 ILE cc_start: 0.6489 (tt) cc_final: 0.6049 (mm) REVERT: M 357 ARG cc_start: 0.8713 (ttp-170) cc_final: 0.8301 (ttp80) REVERT: M 405 ASP cc_start: 0.7831 (p0) cc_final: 0.7590 (p0) REVERT: M 586 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7948 (m-30) outliers start: 15 outliers final: 5 residues processed: 70 average time/residue: 1.2763 time to fit residues: 93.3441 Evaluate side-chains 64 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain M residue 332 ILE Chi-restraints excluded: chain M residue 553 THR Chi-restraints excluded: chain M residue 586 ASP Chi-restraints excluded: chain M residue 588 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 60 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 15 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.4098 r_free = 0.4098 target = 0.180892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.115420 restraints weight = 6077.730| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.53 r_work: 0.3239 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5621 Z= 0.277 Angle : 0.618 7.936 7644 Z= 0.323 Chirality : 0.047 0.154 858 Planarity : 0.006 0.060 981 Dihedral : 5.052 20.151 823 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.30 % Allowed : 10.69 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.91 (0.32), residues: 696 helix: -4.40 (0.47), residues: 26 sheet: 0.32 (0.33), residues: 271 loop : -0.99 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 50 HIS 0.006 0.001 HIS B 92 PHE 0.019 0.002 PHE M 377 TYR 0.011 0.002 TYR B 37 ARG 0.003 0.000 ARG M 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 43 GLN cc_start: 0.8009 (mm-40) cc_final: 0.7404 (mp10) REVERT: A 89 ASP cc_start: 0.8164 (m-30) cc_final: 0.7271 (t0) REVERT: B 117 ILE cc_start: 0.6576 (tt) cc_final: 0.6192 (mm) REVERT: M 357 ARG cc_start: 0.8751 (ttp-170) cc_final: 0.8393 (ttp-170) REVERT: M 403 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.6810 (ttt-90) REVERT: M 405 ASP cc_start: 0.7888 (p0) cc_final: 0.6867 (p0) REVERT: M 461 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7296 (pp) REVERT: M 574 ASP cc_start: 0.7859 (p0) cc_final: 0.7336 (p0) REVERT: M 586 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7853 (m-30) outliers start: 14 outliers final: 7 residues processed: 71 average time/residue: 1.2393 time to fit residues: 92.3881 Evaluate side-chains 71 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain M residue 332 ILE Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 403 ARG Chi-restraints excluded: chain M residue 461 LEU Chi-restraints excluded: chain M residue 470 THR Chi-restraints excluded: chain M residue 553 THR Chi-restraints excluded: chain M residue 586 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 49 optimal weight: 0.3980 chunk 38 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.4107 r_free = 0.4107 target = 0.181744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.116903 restraints weight = 6232.644| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.51 r_work: 0.3257 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 5621 Z= 0.232 Angle : 0.585 7.784 7644 Z= 0.306 Chirality : 0.046 0.146 858 Planarity : 0.005 0.061 981 Dihedral : 4.892 20.831 823 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.63 % Allowed : 13.98 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.83 (0.32), residues: 696 helix: -4.31 (0.51), residues: 26 sheet: 0.43 (0.33), residues: 268 loop : -0.99 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 47 HIS 0.005 0.001 HIS B 92 PHE 0.016 0.001 PHE M 377 TYR 0.009 0.001 TYR B 37 ARG 0.003 0.000 ARG M 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.584 Fit side-chains REVERT: A 43 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7488 (mp10) REVERT: A 89 ASP cc_start: 0.8206 (m-30) cc_final: 0.7334 (t0) REVERT: B 117 ILE cc_start: 0.6616 (tt) cc_final: 0.6248 (mm) REVERT: B 166 GLN cc_start: 0.6918 (tt0) cc_final: 0.6550 (tt0) REVERT: M 357 ARG cc_start: 0.8821 (ttp-170) cc_final: 0.8407 (ttp-170) REVERT: M 403 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.6896 (ttt-90) REVERT: M 405 ASP cc_start: 0.7979 (p0) cc_final: 0.6996 (p0) REVERT: M 461 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7322 (pp) REVERT: M 465 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7834 (tt0) REVERT: M 574 ASP cc_start: 0.7923 (p0) cc_final: 0.7390 (p0) REVERT: M 586 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7939 (m-30) outliers start: 16 outliers final: 8 residues processed: 70 average time/residue: 1.1691 time to fit residues: 85.8899 Evaluate side-chains 72 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain M residue 332 ILE Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 403 ARG Chi-restraints excluded: chain M residue 461 LEU Chi-restraints excluded: chain M residue 465 GLU Chi-restraints excluded: chain M residue 553 THR Chi-restraints excluded: chain M residue 572 THR Chi-restraints excluded: chain M residue 586 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 0.8980 chunk 23 optimal weight: 0.0370 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 57 optimal weight: 0.0050 chunk 60 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 49 optimal weight: 0.2980 overall best weight: 0.4072 ------------------------------------------------------------------------------- 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 = 0.4212 r_free = 0.4212 target = 0.187659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.125077 restraints weight = 6096.801| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.44 r_work: 0.3389 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5621 Z= 0.143 Angle : 0.544 8.393 7644 Z= 0.280 Chirality : 0.044 0.132 858 Planarity : 0.005 0.056 981 Dihedral : 4.528 21.756 823 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.63 % Allowed : 14.64 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.63 (0.32), residues: 696 helix: -4.15 (0.60), residues: 26 sheet: 0.64 (0.33), residues: 262 loop : -0.88 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 47 HIS 0.003 0.001 HIS B 92 PHE 0.009 0.001 PHE M 374 TYR 0.007 0.001 TYR B 140 ARG 0.003 0.000 ARG M 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: A 43 GLN cc_start: 0.8415 (mm-40) cc_final: 0.7905 (mp10) REVERT: A 89 ASP cc_start: 0.8323 (m-30) cc_final: 0.7519 (t0) REVERT: B 117 ILE cc_start: 0.6654 (tt) cc_final: 0.6309 (mm) REVERT: B 166 GLN cc_start: 0.7224 (tt0) cc_final: 0.6842 (tt0) REVERT: M 357 ARG cc_start: 0.8916 (ttp-170) cc_final: 0.8457 (ttp80) REVERT: M 405 ASP cc_start: 0.8093 (p0) cc_final: 0.7822 (p0) REVERT: M 461 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7180 (pp) REVERT: M 586 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8106 (m-30) outliers start: 16 outliers final: 4 residues processed: 71 average time/residue: 1.2435 time to fit residues: 92.4027 Evaluate side-chains 66 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain M residue 332 ILE Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 461 LEU Chi-restraints excluded: chain M residue 586 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN B 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.183583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.120126 restraints weight = 6103.974| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.43 r_work: 0.3326 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5621 Z= 0.329 Angle : 0.658 10.701 7644 Z= 0.342 Chirality : 0.049 0.290 858 Planarity : 0.006 0.061 981 Dihedral : 5.028 20.660 823 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.12 % Allowed : 14.80 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.79 (0.32), residues: 696 helix: -4.20 (0.56), residues: 26 sheet: 0.48 (0.33), residues: 268 loop : -0.98 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 50 HIS 0.006 0.001 HIS B 92 PHE 0.019 0.002 PHE M 377 TYR 0.017 0.002 TYR M 380 ARG 0.003 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 43 GLN cc_start: 0.8519 (mm-40) cc_final: 0.7989 (mp10) REVERT: B 117 ILE cc_start: 0.6783 (tt) cc_final: 0.6437 (mm) REVERT: B 166 GLN cc_start: 0.7237 (tt0) cc_final: 0.6879 (tt0) REVERT: M 403 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7321 (ttt-90) REVERT: M 461 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7558 (pp) REVERT: M 574 ASP cc_start: 0.8094 (p0) cc_final: 0.7719 (p0) REVERT: M 586 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.8203 (m-30) outliers start: 19 outliers final: 9 residues processed: 69 average time/residue: 1.1756 time to fit residues: 85.0202 Evaluate side-chains 69 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain M residue 332 ILE Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 403 ARG Chi-restraints excluded: chain M residue 461 LEU Chi-restraints excluded: chain M residue 572 THR Chi-restraints excluded: chain M residue 581 THR Chi-restraints excluded: chain M residue 586 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 505 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.184119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.120904 restraints weight = 6108.011| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.44 r_work: 0.3335 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5621 Z= 0.279 Angle : 0.661 11.775 7644 Z= 0.339 Chirality : 0.048 0.329 858 Planarity : 0.006 0.062 981 Dihedral : 5.030 20.471 823 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.80 % Allowed : 15.62 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.80 (0.32), residues: 696 helix: -4.22 (0.55), residues: 26 sheet: 0.56 (0.33), residues: 262 loop : -1.03 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 50 HIS 0.006 0.001 HIS B 92 PHE 0.020 0.002 PHE M 377 TYR 0.011 0.001 TYR M 380 ARG 0.004 0.000 ARG M 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 43 GLN cc_start: 0.8447 (mm-40) cc_final: 0.7901 (mp10) REVERT: M 357 ARG cc_start: 0.8909 (ttp-170) cc_final: 0.8532 (ttp-170) REVERT: M 403 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.6878 (ttt-90) REVERT: M 461 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7510 (pp) REVERT: M 574 ASP cc_start: 0.8114 (p0) cc_final: 0.7731 (p0) REVERT: M 586 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.8199 (m-30) outliers start: 17 outliers final: 10 residues processed: 70 average time/residue: 1.4483 time to fit residues: 106.1228 Evaluate side-chains 71 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain M residue 332 ILE Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 403 ARG Chi-restraints excluded: chain M residue 461 LEU Chi-restraints excluded: chain M residue 572 THR Chi-restraints excluded: chain M residue 581 THR Chi-restraints excluded: chain M residue 586 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 37 optimal weight: 0.1980 chunk 50 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.4200 r_free = 0.4200 target = 0.186065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.123412 restraints weight = 6082.861| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.44 r_work: 0.3368 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5621 Z= 0.182 Angle : 0.630 12.480 7644 Z= 0.318 Chirality : 0.046 0.268 858 Planarity : 0.005 0.060 981 Dihedral : 4.765 24.823 823 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.14 % Allowed : 16.78 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.67 (0.32), residues: 696 helix: -4.10 (0.62), residues: 26 sheet: 0.64 (0.33), residues: 261 loop : -0.94 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 47 HIS 0.004 0.001 HIS B 92 PHE 0.015 0.001 PHE M 377 TYR 0.011 0.001 TYR M 380 ARG 0.008 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: A 43 GLN cc_start: 0.8420 (mm-40) cc_final: 0.7883 (mp10) REVERT: A 89 ASP cc_start: 0.8251 (m-30) cc_final: 0.7433 (OUTLIER) REVERT: B 117 ILE cc_start: 0.6777 (tt) cc_final: 0.6402 (mm) REVERT: M 357 ARG cc_start: 0.8920 (ttp-170) cc_final: 0.8509 (ttp80) REVERT: M 403 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.6905 (ttt-90) REVERT: M 405 ASP cc_start: 0.8027 (p0) cc_final: 0.6929 (p0) REVERT: M 461 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7255 (pp) REVERT: M 574 ASP cc_start: 0.8077 (p0) cc_final: 0.7692 (p0) REVERT: M 586 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8152 (m-30) outliers start: 13 outliers final: 10 residues processed: 65 average time/residue: 1.3019 time to fit residues: 88.5001 Evaluate side-chains 70 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain M residue 332 ILE Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 403 ARG Chi-restraints excluded: chain M residue 461 LEU Chi-restraints excluded: chain M residue 572 THR Chi-restraints excluded: chain M residue 581 THR Chi-restraints excluded: chain M residue 586 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 8 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.4187 r_free = 0.4187 target = 0.184720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.121818 restraints weight = 6062.476| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.42 r_work: 0.3346 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5621 Z= 0.242 Angle : 0.657 12.893 7644 Z= 0.332 Chirality : 0.047 0.266 858 Planarity : 0.005 0.060 981 Dihedral : 4.892 26.089 823 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.30 % Allowed : 17.43 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.72 (0.32), residues: 696 helix: -4.11 (0.62), residues: 26 sheet: 0.60 (0.34), residues: 261 loop : -0.97 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 47 HIS 0.005 0.001 HIS B 92 PHE 0.017 0.001 PHE M 377 TYR 0.009 0.001 TYR B 37 ARG 0.005 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.572 Fit side-chains REVERT: A 43 GLN cc_start: 0.8445 (mm-40) cc_final: 0.7906 (mp10) REVERT: A 89 ASP cc_start: 0.8268 (m-30) cc_final: 0.7454 (OUTLIER) REVERT: M 403 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7221 (ttt-90) REVERT: M 461 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7491 (pp) REVERT: M 574 ASP cc_start: 0.8076 (p0) cc_final: 0.7676 (p0) REVERT: M 586 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8209 (m-30) outliers start: 14 outliers final: 11 residues processed: 68 average time/residue: 1.2337 time to fit residues: 87.8950 Evaluate side-chains 68 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain M residue 332 ILE Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 403 ARG Chi-restraints excluded: chain M residue 461 LEU Chi-restraints excluded: chain M residue 572 THR Chi-restraints excluded: chain M residue 581 THR Chi-restraints excluded: chain M residue 586 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 41 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 chunk 18 optimal weight: 6.9990 chunk 44 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 0.0470 chunk 11 optimal weight: 0.5980 overall best weight: 0.9480 ------------------------------------------------------------------------------- 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 = 0.4192 r_free = 0.4192 target = 0.185265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.122328 restraints weight = 6093.052| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.44 r_work: 0.3357 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5621 Z= 0.215 Angle : 0.648 12.149 7644 Z= 0.328 Chirality : 0.046 0.251 858 Planarity : 0.006 0.061 981 Dihedral : 4.827 25.676 823 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.47 % Allowed : 17.76 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.68 (0.32), residues: 696 helix: -4.13 (0.61), residues: 26 sheet: 0.64 (0.34), residues: 261 loop : -0.95 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 47 HIS 0.005 0.001 HIS B 92 PHE 0.015 0.001 PHE M 377 TYR 0.008 0.001 TYR A 159 ARG 0.009 0.000 ARG B 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 43 GLN cc_start: 0.8422 (mm-40) cc_final: 0.7884 (mp10) REVERT: A 89 ASP cc_start: 0.8261 (m-30) cc_final: 0.7454 (OUTLIER) REVERT: M 357 ARG cc_start: 0.8899 (ttp-170) cc_final: 0.8549 (ttp-170) REVERT: M 403 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.6869 (ttt-90) REVERT: M 461 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7299 (pp) REVERT: M 574 ASP cc_start: 0.8080 (p0) cc_final: 0.7680 (p0) REVERT: M 586 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.8186 (m-30) outliers start: 15 outliers final: 11 residues processed: 67 average time/residue: 1.2327 time to fit residues: 86.5187 Evaluate side-chains 68 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain M residue 332 ILE Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 403 ARG Chi-restraints excluded: chain M residue 461 LEU Chi-restraints excluded: chain M residue 572 THR Chi-restraints excluded: chain M residue 581 THR Chi-restraints excluded: chain M residue 586 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 0.0870 chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 overall best weight: 1.7962 ------------------------------------------------------------------------------- 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 = 0.4172 r_free = 0.4172 target = 0.183267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.119849 restraints weight = 6107.003| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.45 r_work: 0.3323 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 5621 Z= 0.336 Angle : 0.720 13.392 7644 Z= 0.365 Chirality : 0.049 0.285 858 Planarity : 0.006 0.064 981 Dihedral : 5.240 26.672 823 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.47 % Allowed : 17.76 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.81 (0.32), residues: 696 helix: -4.19 (0.57), residues: 26 sheet: 0.56 (0.34), residues: 261 loop : -1.05 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 50 HIS 0.006 0.001 HIS B 92 PHE 0.021 0.002 PHE M 377 TYR 0.014 0.002 TYR M 396 ARG 0.008 0.000 ARG B 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6989.90 seconds wall clock time: 121 minutes 37.89 seconds (7297.89 seconds total)