Starting phenix.real_space_refine on Mon Jan 13 23:08:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k18_36788/01_2025/8k18_36788.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k18_36788/01_2025/8k18_36788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k18_36788/01_2025/8k18_36788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k18_36788/01_2025/8k18_36788.map" model { file = "/net/cci-nas-00/data/ceres_data/8k18_36788/01_2025/8k18_36788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k18_36788/01_2025/8k18_36788.cif" } resolution = 3.68 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= 0.019 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 1444 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 16 5.16 5 C 2063 2.51 5 N 541 2.21 5 O 626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 3246 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 1505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1505 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 10, 'TRANS': 177} Chain breaks: 1 Chain: "C" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 931 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 113} Chain: "D" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Time building chain proxies: 3.42, per 1000 atoms: 1.05 Number of scatterers: 3246 At special positions: 0 Unit cell: (64.66, 64.66, 92.22, 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 16 16.00 O 626 8.00 N 541 7.00 C 2063 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.01 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.05 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 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 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 456.0 milliseconds 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 754 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 9 sheets defined 12.1% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.891A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 368 Processing helix chain 'E' and resid 405 through 410 Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'C' and resid 28 through 32 removed outlier: 4.042A pdb=" N ARG C 31 " --> pdb=" O ILE C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.747A pdb=" N ILE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.932A pdb=" N GLU E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER E 399 " --> pdb=" O GLU E 354 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS E 356 " --> pdb=" O ALA E 397 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE E 392 " --> pdb=" O VAL E 524 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL E 524 " --> pdb=" O PHE E 392 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.932A pdb=" N GLU E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER E 399 " --> pdb=" O GLU E 354 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS E 356 " --> pdb=" O ALA E 397 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 452 through 454 removed outlier: 3.577A pdb=" N TYR E 453 " --> pdb=" O GLN E 493 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.800A pdb=" N THR C 113 " --> pdb=" O TYR C 93 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR C 93 " --> pdb=" O THR C 113 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N THR C 92 " --> pdb=" O GLN C 39 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET C 34 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ILE C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 17 through 20 removed outlier: 3.511A pdb=" N LEU C 20 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU C 80 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.701A pdb=" N VAL D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.500A pdb=" N GLU D 105 " --> pdb=" O LEU D 11 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.646A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) 95 hydrogen bonds defined for protein. 231 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.87 Time building geometry restraints manager: 1.10 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: 627 1.32 - 1.45: 880 1.45 - 1.57: 1799 1.57 - 1.70: 0 1.70 - 1.82: 20 Bond restraints: 3326 Sorted by residual: bond pdb=" N GLY C 91 " pdb=" CA GLY C 91 " ideal model delta sigma weight residual 1.444 1.478 -0.034 9.10e-03 1.21e+04 1.38e+01 bond pdb=" CZ ARG C 38 " pdb=" NH2 ARG C 38 " ideal model delta sigma weight residual 1.330 1.283 0.047 1.30e-02 5.92e+03 1.30e+01 bond pdb=" CZ ARG C 71 " pdb=" NH1 ARG C 71 " ideal model delta sigma weight residual 1.323 1.278 0.045 1.40e-02 5.10e+03 1.02e+01 bond pdb=" N VAL E 483 " pdb=" CA VAL E 483 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.23e-02 6.61e+03 9.87e+00 bond pdb=" CA PHE E 515 " pdb=" C PHE E 515 " ideal model delta sigma weight residual 1.524 1.562 -0.038 1.25e-02 6.40e+03 9.48e+00 ... (remaining 3321 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 3178 1.84 - 3.68: 1098 3.68 - 5.53: 200 5.53 - 7.37: 33 7.37 - 9.21: 5 Bond angle restraints: 4514 Sorted by residual: angle pdb=" NE ARG C 71 " pdb=" CZ ARG C 71 " pdb=" NH2 ARG C 71 " ideal model delta sigma weight residual 119.20 126.52 -7.32 9.00e-01 1.23e+00 6.62e+01 angle pdb=" CA GLY C 91 " pdb=" C GLY C 91 " pdb=" N THR C 92 " ideal model delta sigma weight residual 114.50 122.53 -8.03 1.19e+00 7.06e-01 4.56e+01 angle pdb=" O GLY C 91 " pdb=" C GLY C 91 " pdb=" N THR C 92 " ideal model delta sigma weight residual 123.59 117.81 5.78 8.70e-01 1.32e+00 4.41e+01 angle pdb=" OE1 GLN D 27 " pdb=" CD GLN D 27 " pdb=" NE2 GLN D 27 " ideal model delta sigma weight residual 122.60 116.03 6.57 1.00e+00 1.00e+00 4.32e+01 angle pdb=" CA PHE E 515 " pdb=" CB PHE E 515 " pdb=" CG PHE E 515 " ideal model delta sigma weight residual 113.80 119.75 -5.95 1.00e+00 1.00e+00 3.54e+01 ... (remaining 4509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.82: 1737 15.82 - 31.64: 152 31.64 - 47.46: 47 47.46 - 63.28: 11 63.28 - 79.10: 4 Dihedral angle restraints: 1951 sinusoidal: 761 harmonic: 1190 Sorted by residual: dihedral pdb=" CD ARG E 457 " pdb=" NE ARG E 457 " pdb=" CZ ARG E 457 " pdb=" NH1 ARG E 457 " ideal model delta sinusoidal sigma weight residual 0.00 67.40 -67.40 1 1.00e+01 1.00e-02 5.91e+01 dihedral pdb=" CD ARG C 103 " pdb=" NE ARG C 103 " pdb=" CZ ARG C 103 " pdb=" NH1 ARG C 103 " ideal model delta sinusoidal sigma weight residual 0.00 -39.95 39.95 1 1.00e+01 1.00e-02 2.24e+01 dihedral pdb=" CB CYS E 336 " pdb=" SG CYS E 336 " pdb=" SG CYS E 361 " pdb=" CB CYS E 361 " ideal model delta sinusoidal sigma weight residual -86.00 -123.61 37.61 1 1.00e+01 1.00e-02 1.99e+01 ... (remaining 1948 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 234 0.059 - 0.117: 159 0.117 - 0.175: 65 0.175 - 0.233: 20 0.233 - 0.291: 4 Chirality restraints: 482 Sorted by residual: chirality pdb=" CA THR C 92 " pdb=" N THR C 92 " pdb=" C THR C 92 " pdb=" CB THR C 92 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CB VAL C 29 " pdb=" CA VAL C 29 " pdb=" CG1 VAL C 29 " pdb=" CG2 VAL C 29 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA ASP E 427 " pdb=" N ASP E 427 " pdb=" C ASP E 427 " pdb=" CB ASP E 427 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 479 not shown) Planarity restraints: 586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 109 " -0.150 2.00e-02 2.50e+03 8.15e-02 1.66e+02 pdb=" CG TRP C 109 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP C 109 " 0.117 2.00e-02 2.50e+03 pdb=" CD2 TRP C 109 " 0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP C 109 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TRP C 109 " -0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP C 109 " 0.071 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 109 " -0.115 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 109 " 0.081 2.00e-02 2.50e+03 pdb=" CH2 TRP C 109 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 457 " -1.003 9.50e-02 1.11e+02 4.50e-01 1.22e+02 pdb=" NE ARG E 457 " 0.061 2.00e-02 2.50e+03 pdb=" CZ ARG E 457 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG E 457 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG E 457 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 449 " 0.110 2.00e-02 2.50e+03 7.74e-02 1.20e+02 pdb=" CG TYR E 449 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR E 449 " -0.043 2.00e-02 2.50e+03 pdb=" CD2 TYR E 449 " -0.053 2.00e-02 2.50e+03 pdb=" CE1 TYR E 449 " -0.071 2.00e-02 2.50e+03 pdb=" CE2 TYR E 449 " -0.063 2.00e-02 2.50e+03 pdb=" CZ TYR E 449 " -0.030 2.00e-02 2.50e+03 pdb=" OH TYR E 449 " 0.145 2.00e-02 2.50e+03 ... (remaining 583 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 9 2.58 - 3.16: 2495 3.16 - 3.74: 5033 3.74 - 4.32: 7191 4.32 - 4.90: 11493 Nonbonded interactions: 26221 Sorted by model distance: nonbonded pdb=" CG ARG E 355 " pdb=" OD1 ASP E 398 " model vdw 1.995 3.440 nonbonded pdb=" OD1 ASN E 417 " pdb=" CE2 TYR C 52 " model vdw 1.999 3.340 nonbonded pdb=" OD2 ASP E 420 " pdb=" OG SER C 56 " model vdw 2.093 3.040 nonbonded pdb=" CG2 VAL C 24 " pdb=" CG2 VAL C 29 " model vdw 2.424 3.880 nonbonded pdb=" ND2 ASN E 481 " pdb=" CG2 VAL E 483 " model vdw 2.433 3.540 ... (remaining 26216 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: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 13.630 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3435 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 : 0.014 0.047 3326 Z= 0.918 Angle : 1.855 9.208 4514 Z= 1.237 Chirality : 0.089 0.291 482 Planarity : 0.034 0.450 586 Dihedral : 13.981 79.096 1185 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.85 % Allowed : 8.73 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % 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: -1.91 (0.40), residues: 406 helix: -4.07 (0.61), residues: 24 sheet: -1.36 (0.48), residues: 89 loop : -1.00 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.150 0.027 TRP C 109 HIS 0.025 0.008 HIS D 93 PHE 0.069 0.014 PHE E 497 TYR 0.145 0.026 TYR E 449 ARG 0.015 0.003 ARG C 31 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 33 average time/residue: 0.3314 time to fit residues: 12.6113 Evaluate side-chains 13 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 457 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 20.0000 chunk 29 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 30 optimal weight: 50.0000 chunk 11 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 GLN ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.037546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.026771 restraints weight = 485221.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.026626 restraints weight = 562506.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.026455 restraints weight = 529476.147| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 3326 Z= 0.356 Angle : 0.775 9.320 4514 Z= 0.416 Chirality : 0.048 0.262 482 Planarity : 0.006 0.050 586 Dihedral : 6.223 44.723 459 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 21.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.10 % Allowed : 12.11 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % 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: -1.50 (0.41), residues: 406 helix: -3.42 (1.09), residues: 12 sheet: -1.63 (0.44), residues: 112 loop : -0.55 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP D 35 HIS 0.003 0.001 HIS D 93 PHE 0.020 0.002 PHE E 371 TYR 0.017 0.002 TYR E 365 ARG 0.006 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 14 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 347 PHE cc_start: 0.7343 (OUTLIER) cc_final: 0.6081 (m-80) REVERT: E 449 TYR cc_start: 0.8275 (OUTLIER) cc_final: 0.7788 (m-80) outliers start: 11 outliers final: 6 residues processed: 24 average time/residue: 0.2825 time to fit residues: 7.9910 Evaluate side-chains 20 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 12 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 449 TYR Chi-restraints excluded: chain E residue 457 ARG Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 106 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 35 optimal weight: 50.0000 chunk 38 optimal weight: 30.0000 chunk 31 optimal weight: 40.0000 chunk 12 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.036998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.032080 restraints weight = 45689.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.031450 restraints weight = 132370.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.031219 restraints weight = 155994.685| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.5783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3326 Z= 0.243 Angle : 0.676 8.936 4514 Z= 0.355 Chirality : 0.044 0.193 482 Planarity : 0.005 0.038 586 Dihedral : 5.744 33.766 459 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 21.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.25 % Allowed : 15.49 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % 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: -1.44 (0.41), residues: 406 helix: -2.76 (1.23), residues: 12 sheet: -1.43 (0.44), residues: 115 loop : -0.62 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 35 HIS 0.002 0.001 HIS D 70 PHE 0.023 0.002 PHE E 392 TYR 0.017 0.002 TYR E 501 ARG 0.005 0.001 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 14 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 449 TYR cc_start: 0.8159 (OUTLIER) cc_final: 0.7907 (m-80) REVERT: D 18 ARG cc_start: 0.6739 (tpp80) cc_final: 0.6021 (tpp80) outliers start: 8 outliers final: 4 residues processed: 20 average time/residue: 0.2756 time to fit residues: 6.6236 Evaluate side-chains 18 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 13 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 449 TYR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 14 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 50.0000 chunk 7 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.036616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.031444 restraints weight = 45636.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.031054 restraints weight = 130648.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.030769 restraints weight = 131798.547| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.6603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3326 Z= 0.249 Angle : 0.678 8.426 4514 Z= 0.354 Chirality : 0.044 0.175 482 Planarity : 0.005 0.033 586 Dihedral : 5.344 18.188 455 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 24.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.82 % Allowed : 16.62 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % 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: -1.39 (0.42), residues: 406 helix: -2.73 (1.10), residues: 18 sheet: -1.22 (0.48), residues: 111 loop : -0.63 (0.39), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 35 HIS 0.002 0.001 HIS D 70 PHE 0.020 0.002 PHE E 392 TYR 0.014 0.002 TYR E 501 ARG 0.005 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 11 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 449 TYR cc_start: 0.8289 (OUTLIER) cc_final: 0.8039 (m-80) REVERT: D 4 MET cc_start: 0.3683 (ttt) cc_final: 0.3358 (ttt) outliers start: 10 outliers final: 5 residues processed: 21 average time/residue: 0.2425 time to fit residues: 6.1900 Evaluate side-chains 16 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 10 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 449 TYR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 30 optimal weight: 6.9990 chunk 15 optimal weight: 20.0000 chunk 5 optimal weight: 0.7980 chunk 14 optimal weight: 40.0000 chunk 19 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 chunk 6 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 overall best weight: 4.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.036385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.032104 restraints weight = 46698.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.031860 restraints weight = 135758.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.031663 restraints weight = 150140.684| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.6889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3326 Z= 0.198 Angle : 0.643 8.538 4514 Z= 0.337 Chirality : 0.044 0.163 482 Planarity : 0.005 0.031 586 Dihedral : 5.164 18.833 455 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 22.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.10 % Allowed : 17.75 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % 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: -1.26 (0.43), residues: 406 helix: -2.66 (1.06), residues: 18 sheet: -1.20 (0.46), residues: 116 loop : -0.47 (0.41), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 35 HIS 0.002 0.001 HIS D 70 PHE 0.021 0.002 PHE E 392 TYR 0.016 0.002 TYR E 501 ARG 0.006 0.001 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 11 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 MET cc_start: 0.3481 (ttt) cc_final: 0.1775 (tpt) outliers start: 11 outliers final: 7 residues processed: 22 average time/residue: 0.2251 time to fit residues: 6.3130 Evaluate side-chains 18 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 11 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 457 ARG Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 50.0000 chunk 22 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 15 optimal weight: 20.0000 chunk 18 optimal weight: 0.0670 chunk 26 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 overall best weight: 4.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.035925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.030904 restraints weight = 47489.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.030639 restraints weight = 138619.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.030484 restraints weight = 139316.724| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.7494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3326 Z= 0.204 Angle : 0.644 9.537 4514 Z= 0.339 Chirality : 0.044 0.147 482 Planarity : 0.005 0.031 586 Dihedral : 5.030 17.567 455 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 22.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.54 % Allowed : 19.15 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % 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: -1.27 (0.43), residues: 406 helix: -2.27 (1.11), residues: 24 sheet: -1.49 (0.46), residues: 117 loop : -0.29 (0.41), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 35 HIS 0.002 0.001 HIS D 70 PHE 0.023 0.002 PHE E 392 TYR 0.014 0.002 TYR E 501 ARG 0.004 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 13 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 MET cc_start: 0.4021 (ttt) cc_final: 0.1964 (tpt) outliers start: 9 outliers final: 6 residues processed: 22 average time/residue: 0.3175 time to fit residues: 8.2528 Evaluate side-chains 17 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 11 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 457 ARG Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 16 optimal weight: 10.0000 chunk 8 optimal weight: 30.0000 chunk 17 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 40.0000 chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 38 optimal weight: 50.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.035595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.030809 restraints weight = 48351.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.030537 restraints weight = 125909.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.030422 restraints weight = 140847.698| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.8114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3326 Z= 0.247 Angle : 0.715 10.120 4514 Z= 0.370 Chirality : 0.045 0.136 482 Planarity : 0.005 0.038 586 Dihedral : 5.232 16.896 455 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 27.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.54 % Allowed : 20.28 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % 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: -1.29 (0.43), residues: 406 helix: -2.41 (1.08), residues: 24 sheet: -1.41 (0.48), residues: 117 loop : -0.35 (0.41), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 35 HIS 0.002 0.001 HIS D 70 PHE 0.019 0.002 PHE E 392 TYR 0.015 0.002 TYR C 93 ARG 0.004 0.001 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 11 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 MET cc_start: 0.4568 (ttt) cc_final: 0.2550 (tpt) outliers start: 9 outliers final: 7 residues processed: 20 average time/residue: 0.2272 time to fit residues: 5.6579 Evaluate side-chains 18 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 11 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 457 ARG Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 40.0000 chunk 26 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 chunk 28 optimal weight: 40.0000 chunk 32 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.035197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.031511 restraints weight = 48469.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.031132 restraints weight = 120898.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.031039 restraints weight = 139126.577| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.8636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3326 Z= 0.242 Angle : 0.696 8.931 4514 Z= 0.364 Chirality : 0.045 0.178 482 Planarity : 0.005 0.031 586 Dihedral : 5.230 16.468 455 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 28.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.82 % Allowed : 19.72 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % 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: -1.26 (0.44), residues: 406 helix: -2.26 (1.12), residues: 24 sheet: -1.48 (0.47), residues: 116 loop : -0.30 (0.41), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 35 HIS 0.003 0.001 HIS E 505 PHE 0.020 0.002 PHE E 392 TYR 0.017 0.002 TYR E 501 ARG 0.004 0.001 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 11 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 MET cc_start: 0.4669 (ttt) cc_final: 0.2218 (tpt) outliers start: 10 outliers final: 7 residues processed: 21 average time/residue: 0.2345 time to fit residues: 6.0676 Evaluate side-chains 18 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 11 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 457 ARG Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.945 > 50: distance: 3 - 16: 10.169 distance: 12 - 16: 7.279 distance: 16 - 17: 4.581 distance: 17 - 18: 17.050 distance: 17 - 20: 16.920 distance: 18 - 19: 7.754 distance: 18 - 24: 30.841 distance: 20 - 21: 14.232 distance: 21 - 22: 4.730 distance: 21 - 23: 3.611 distance: 24 - 25: 21.945 distance: 25 - 26: 14.542 distance: 25 - 28: 38.626 distance: 26 - 27: 4.247 distance: 26 - 29: 30.818 distance: 29 - 30: 23.623 distance: 30 - 31: 26.647 distance: 30 - 33: 22.402 distance: 31 - 32: 10.995 distance: 31 - 36: 13.183 distance: 33 - 34: 21.985 distance: 33 - 35: 10.205 distance: 36 - 37: 10.940 distance: 37 - 38: 16.612 distance: 37 - 40: 5.786 distance: 38 - 39: 18.779 distance: 38 - 45: 7.777 distance: 40 - 41: 8.946 distance: 41 - 42: 12.420 distance: 42 - 43: 14.311 distance: 43 - 44: 11.732 distance: 45 - 46: 13.004 distance: 46 - 47: 3.522 distance: 46 - 49: 14.506 distance: 47 - 48: 15.141 distance: 47 - 56: 8.166 distance: 49 - 50: 7.199 distance: 50 - 51: 6.070 distance: 50 - 52: 17.353 distance: 51 - 53: 6.831 distance: 52 - 54: 6.545 distance: 53 - 55: 17.219 distance: 54 - 55: 8.435 distance: 56 - 57: 6.930 distance: 56 - 62: 14.980 distance: 57 - 58: 16.137 distance: 57 - 60: 14.926 distance: 58 - 59: 8.967 distance: 60 - 61: 10.771 distance: 61 - 62: 9.515 distance: 63 - 64: 14.203 distance: 64 - 65: 6.649 distance: 64 - 67: 15.162 distance: 65 - 66: 11.613 distance: 65 - 69: 15.067 distance: 66 - 88: 5.405 distance: 67 - 68: 12.182 distance: 69 - 70: 10.393 distance: 70 - 73: 6.997 distance: 71 - 72: 9.760 distance: 73 - 74: 8.870 distance: 73 - 75: 8.161 distance: 76 - 77: 3.940 distance: 77 - 78: 6.904 distance: 77 - 80: 6.194 distance: 78 - 79: 4.990 distance: 78 - 88: 6.646 distance: 80 - 81: 3.739 distance: 81 - 83: 7.244 distance: 82 - 84: 4.208 distance: 83 - 85: 4.788 distance: 85 - 86: 5.167 distance: 86 - 87: 5.023 distance: 88 - 89: 8.036 distance: 89 - 90: 5.004 distance: 89 - 92: 12.691 distance: 90 - 91: 3.029