Starting phenix.real_space_refine on Fri Aug 22 14:02:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n9a_24253/08_2025/7n9a_24253.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n9a_24253/08_2025/7n9a_24253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7n9a_24253/08_2025/7n9a_24253.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n9a_24253/08_2025/7n9a_24253.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n9a_24253/08_2025/7n9a_24253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n9a_24253/08_2025/7n9a_24253.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 1545 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 11 5.16 5 C 1540 2.51 5 N 420 2.21 5 O 460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2431 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 886 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "E" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1545 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Time building chain proxies: 0.98, per 1000 atoms: 0.40 Number of scatterers: 2431 At special positions: 0 Unit cell: (79.68, 60.59, 79.68, 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 11 16.00 O 460 8.00 N 420 7.00 C 1540 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 94 " distance=2.05 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " 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: 0.17 Conformation dependent library (CDL) restraints added in 82.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 564 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 5 sheets defined 13.5% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 85 through 89 removed outlier: 3.524A pdb=" N THR A 89 " --> pdb=" O PRO A 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 343 removed outlier: 3.580A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 371 removed outlier: 4.099A pdb=" N LEU E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 390 removed outlier: 3.817A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP E 389 " --> pdb=" O LYS E 386 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU E 390 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 408 removed outlier: 4.382A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 405 through 408' Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.544A pdb=" N SER A 7 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER A 21 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR A 67 " --> pdb=" O GLN A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.786A pdb=" N VAL A 113 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 90 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 91 " --> pdb=" O ARG A 37 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ARG A 36 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE A 45 " --> pdb=" O ARG A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.786A pdb=" N VAL A 113 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 90 " --> pdb=" O VAL A 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.597A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454 66 hydrogen bonds defined for protein. 171 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: 0.31 Time building geometry restraints manager: 0.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 796 1.34 - 1.47: 657 1.47 - 1.59: 1025 1.59 - 1.71: 0 1.71 - 1.84: 12 Bond restraints: 2490 Sorted by residual: bond pdb=" N PRO E 499 " pdb=" CD PRO E 499 " ideal model delta sigma weight residual 1.473 1.446 0.027 1.40e-02 5.10e+03 3.76e+00 bond pdb=" CB VAL A 2 " pdb=" CG1 VAL A 2 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.78e+00 bond pdb=" CA PRO E 499 " pdb=" CB PRO E 499 " ideal model delta sigma weight residual 1.534 1.558 -0.024 1.49e-02 4.50e+03 2.65e+00 bond pdb=" CG LEU E 518 " pdb=" CD1 LEU E 518 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.56e+00 bond pdb=" CB PHE A 45 " pdb=" CG PHE A 45 " ideal model delta sigma weight residual 1.502 1.467 0.035 2.30e-02 1.89e+03 2.36e+00 ... (remaining 2485 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 3149 2.28 - 4.55: 185 4.55 - 6.83: 37 6.83 - 9.11: 5 9.11 - 11.39: 5 Bond angle restraints: 3381 Sorted by residual: angle pdb=" CA PRO E 499 " pdb=" N PRO E 499 " pdb=" CD PRO E 499 " ideal model delta sigma weight residual 112.00 102.71 9.29 1.40e+00 5.10e-01 4.40e+01 angle pdb=" N GLY E 482 " pdb=" CA GLY E 482 " pdb=" C GLY E 482 " ideal model delta sigma weight residual 114.90 122.64 -7.74 1.54e+00 4.22e-01 2.53e+01 angle pdb=" CA CYS A 22 " pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " ideal model delta sigma weight residual 114.40 125.79 -11.39 2.30e+00 1.89e-01 2.45e+01 angle pdb=" C GLN E 409 " pdb=" N ILE E 410 " pdb=" CA ILE E 410 " ideal model delta sigma weight residual 123.11 117.10 6.01 1.36e+00 5.41e-01 1.95e+01 angle pdb=" CA TYR E 495 " pdb=" CB TYR E 495 " pdb=" CG TYR E 495 " ideal model delta sigma weight residual 113.90 121.76 -7.86 1.80e+00 3.09e-01 1.91e+01 ... (remaining 3376 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.68: 1342 16.68 - 33.36: 93 33.36 - 50.04: 20 50.04 - 66.72: 5 66.72 - 83.40: 4 Dihedral angle restraints: 1464 sinusoidal: 569 harmonic: 895 Sorted by residual: dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 94 " pdb=" CB CYS A 94 " ideal model delta sinusoidal sigma weight residual 93.00 165.21 -72.21 1 1.00e+01 1.00e-02 6.67e+01 dihedral pdb=" CB CYS E 480 " pdb=" SG CYS E 480 " pdb=" SG CYS E 488 " pdb=" CB CYS E 488 " ideal model delta sinusoidal sigma weight residual 93.00 145.12 -52.12 1 1.00e+01 1.00e-02 3.71e+01 dihedral pdb=" SG CYS E 391 " pdb=" CB CYS E 525 " pdb=" SG CYS E 525 " pdb=" CA CYS E 525 " ideal model delta sinusoidal sigma weight residual -73.00 -14.99 -58.01 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 1461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 202 0.045 - 0.090: 101 0.090 - 0.136: 39 0.136 - 0.181: 12 0.181 - 0.226: 4 Chirality restraints: 358 Sorted by residual: chirality pdb=" CA ASN E 481 " pdb=" N ASN E 481 " pdb=" C ASN E 481 " pdb=" CB ASN E 481 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA PHE E 497 " pdb=" N PHE E 497 " pdb=" C PHE E 497 " pdb=" CB PHE E 497 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CG LEU E 455 " pdb=" CB LEU E 455 " pdb=" CD1 LEU E 455 " pdb=" CD2 LEU E 455 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.65e-01 ... (remaining 355 not shown) Planarity restraints: 445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 498 " 0.067 5.00e-02 4.00e+02 9.57e-02 1.46e+01 pdb=" N PRO E 499 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO E 499 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO E 499 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 495 " -0.026 2.00e-02 2.50e+03 2.25e-02 1.01e+01 pdb=" CG TYR E 495 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR E 495 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR E 495 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR E 495 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR E 495 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR E 495 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 495 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 497 " 0.003 2.00e-02 2.50e+03 2.34e-02 9.60e+00 pdb=" CG PHE E 497 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE E 497 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 PHE E 497 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE E 497 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 PHE E 497 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE E 497 " 0.000 2.00e-02 2.50e+03 ... (remaining 442 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 75 2.69 - 3.24: 2344 3.24 - 3.79: 3625 3.79 - 4.35: 4704 4.35 - 4.90: 7651 Nonbonded interactions: 18399 Sorted by model distance: nonbonded pdb=" O THR A 101 " pdb=" OH TYR E 489 " model vdw 2.135 3.040 nonbonded pdb=" OD1 ASN E 448 " pdb=" ND2 ASN E 450 " model vdw 2.182 3.120 nonbonded pdb=" O GLN E 414 " pdb=" NZ LYS E 424 " model vdw 2.246 3.120 nonbonded pdb=" O ASN A 72 " pdb=" ND2 ASN A 72 " model vdw 2.315 3.120 nonbonded pdb=" OD1 ASN E 388 " pdb=" N ASP E 389 " model vdw 2.316 3.120 ... (remaining 18394 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: 8.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.490 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 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 : 0.007 0.055 2495 Z= 0.301 Angle : 1.287 13.720 3391 Z= 0.745 Chirality : 0.064 0.226 358 Planarity : 0.007 0.096 445 Dihedral : 12.630 83.395 885 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.45), residues: 308 helix: -2.13 (0.71), residues: 30 sheet: 1.69 (0.55), residues: 74 loop : -0.48 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 43 TYR 0.056 0.005 TYR E 495 PHE 0.042 0.004 PHE E 497 TRP 0.010 0.003 TRP E 353 HIS 0.005 0.002 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00693 ( 2490) covalent geometry : angle 1.25857 ( 3381) SS BOND : bond 0.00864 ( 5) SS BOND : angle 5.13315 ( 10) hydrogen bonds : bond 0.29651 ( 62) hydrogen bonds : angle 10.02280 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.113 Fit side-chains REVERT: A 42 GLU cc_start: 0.7168 (tm-30) cc_final: 0.6715 (tm-30) REVERT: E 489 TYR cc_start: 0.6940 (m-80) cc_final: 0.6408 (m-80) REVERT: E 501 ASN cc_start: 0.7721 (m110) cc_final: 0.7519 (m110) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0456 time to fit residues: 4.2035 Evaluate side-chains 66 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 28 optimal weight: 0.1980 chunk 13 optimal weight: 0.2980 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 chunk 16 optimal weight: 0.3980 chunk 15 optimal weight: 0.4980 chunk 29 optimal weight: 0.4980 chunk 25 optimal weight: 0.3980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN A 72 ASN A 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.143258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.130649 restraints weight = 4409.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.134477 restraints weight = 2397.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.137036 restraints weight = 1443.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.138794 restraints weight = 925.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.140017 restraints weight = 618.477| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 2495 Z= 0.232 Angle : 0.713 6.914 3391 Z= 0.392 Chirality : 0.049 0.135 358 Planarity : 0.005 0.037 445 Dihedral : 5.771 18.865 349 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.10 % Allowed : 10.08 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.45), residues: 308 helix: -2.56 (0.71), residues: 31 sheet: 1.39 (0.55), residues: 79 loop : -0.66 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 43 TYR 0.019 0.003 TYR E 473 PHE 0.018 0.002 PHE E 497 TRP 0.012 0.003 TRP A 107 HIS 0.003 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 2490) covalent geometry : angle 0.70841 ( 3381) SS BOND : bond 0.00535 ( 5) SS BOND : angle 1.60615 ( 10) hydrogen bonds : bond 0.05055 ( 62) hydrogen bonds : angle 7.56533 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.096 Fit side-chains REVERT: A 42 GLU cc_start: 0.7177 (tm-30) cc_final: 0.6815 (tm-30) REVERT: E 395 VAL cc_start: 0.7870 (m) cc_final: 0.7597 (t) outliers start: 8 outliers final: 4 residues processed: 68 average time/residue: 0.0473 time to fit residues: 4.0382 Evaluate side-chains 69 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 385 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 10 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 0.0980 chunk 5 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 28 optimal weight: 0.0870 chunk 14 optimal weight: 0.1980 chunk 12 optimal weight: 0.6980 chunk 21 optimal weight: 0.2980 overall best weight: 0.2158 ------------------------------------------------------------------------------- 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 = 0.3929 r_free = 0.3929 target = 0.144968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.131753 restraints weight = 4485.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.135820 restraints weight = 2392.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.138525 restraints weight = 1424.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.140391 restraints weight = 906.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.141644 restraints weight = 600.443| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2495 Z= 0.164 Angle : 0.602 6.250 3391 Z= 0.328 Chirality : 0.046 0.145 358 Planarity : 0.005 0.040 445 Dihedral : 5.286 18.722 349 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 5.04 % Allowed : 12.79 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.45), residues: 308 helix: -2.54 (0.75), residues: 29 sheet: 0.79 (0.57), residues: 73 loop : -0.57 (0.41), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 70 TYR 0.016 0.002 TYR E 449 PHE 0.030 0.003 PHE E 497 TRP 0.010 0.002 TRP A 34 HIS 0.003 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 2490) covalent geometry : angle 0.59980 ( 3381) SS BOND : bond 0.00270 ( 5) SS BOND : angle 1.19028 ( 10) hydrogen bonds : bond 0.03889 ( 62) hydrogen bonds : angle 7.11622 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.107 Fit side-chains REVERT: A 42 GLU cc_start: 0.7219 (tm-30) cc_final: 0.6877 (tm-30) REVERT: E 395 VAL cc_start: 0.7731 (OUTLIER) cc_final: 0.7489 (t) outliers start: 13 outliers final: 8 residues processed: 69 average time/residue: 0.0430 time to fit residues: 3.8064 Evaluate side-chains 70 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 500 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 0.4980 chunk 26 optimal weight: 0.0870 chunk 1 optimal weight: 0.6980 chunk 16 optimal weight: 0.0770 chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 25 optimal weight: 0.0870 chunk 28 optimal weight: 0.0050 chunk 18 optimal weight: 0.0870 chunk 4 optimal weight: 0.9990 overall best weight: 0.0686 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.147320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.134861 restraints weight = 4365.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.138696 restraints weight = 2349.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.141322 restraints weight = 1404.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.143102 restraints weight = 886.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.144281 restraints weight = 583.496| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2495 Z= 0.107 Angle : 0.579 9.496 3391 Z= 0.301 Chirality : 0.045 0.147 358 Planarity : 0.005 0.042 445 Dihedral : 4.870 17.359 349 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.88 % Allowed : 15.50 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.44), residues: 308 helix: -2.48 (0.79), residues: 29 sheet: 0.66 (0.57), residues: 73 loop : -0.53 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 43 TYR 0.013 0.001 TYR A 106 PHE 0.035 0.002 PHE E 497 TRP 0.014 0.002 TRP A 107 HIS 0.001 0.000 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 2490) covalent geometry : angle 0.57779 ( 3381) SS BOND : bond 0.00212 ( 5) SS BOND : angle 0.94467 ( 10) hydrogen bonds : bond 0.03398 ( 62) hydrogen bonds : angle 6.63521 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.088 Fit side-chains REVERT: A 42 GLU cc_start: 0.7107 (tm-30) cc_final: 0.6769 (tm-30) outliers start: 10 outliers final: 9 residues processed: 69 average time/residue: 0.0461 time to fit residues: 4.0069 Evaluate side-chains 70 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 518 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 7 optimal weight: 0.0980 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.140520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.127599 restraints weight = 4379.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.131476 restraints weight = 2403.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.134080 restraints weight = 1453.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.135908 restraints weight = 936.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.137118 restraints weight = 625.016| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 2495 Z= 0.285 Angle : 0.679 6.722 3391 Z= 0.367 Chirality : 0.048 0.144 358 Planarity : 0.005 0.038 445 Dihedral : 5.656 19.442 349 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 6.98 % Allowed : 17.05 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.45), residues: 308 helix: -2.60 (0.85), residues: 29 sheet: 0.49 (0.53), residues: 79 loop : -0.67 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 43 TYR 0.021 0.003 TYR E 453 PHE 0.048 0.003 PHE E 497 TRP 0.012 0.003 TRP A 107 HIS 0.004 0.002 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00636 ( 2490) covalent geometry : angle 0.67703 ( 3381) SS BOND : bond 0.00275 ( 5) SS BOND : angle 1.21351 ( 10) hydrogen bonds : bond 0.04319 ( 62) hydrogen bonds : angle 6.75252 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.095 Fit side-chains REVERT: A 42 GLU cc_start: 0.7255 (tm-30) cc_final: 0.6981 (tm-30) REVERT: A 97 ARG cc_start: 0.7691 (ptm-80) cc_final: 0.7357 (ptm-80) REVERT: E 421 TYR cc_start: 0.8146 (m-80) cc_final: 0.7941 (m-80) outliers start: 18 outliers final: 14 residues processed: 67 average time/residue: 0.0518 time to fit residues: 4.2232 Evaluate side-chains 76 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 518 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 0.0670 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.0980 chunk 11 optimal weight: 0.4980 chunk 26 optimal weight: 0.3980 chunk 25 optimal weight: 0.3980 chunk 7 optimal weight: 0.3980 chunk 12 optimal weight: 0.1980 chunk 23 optimal weight: 0.2980 chunk 4 optimal weight: 0.0980 overall best weight: 0.1518 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.143719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.130252 restraints weight = 4363.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.134334 restraints weight = 2352.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.137060 restraints weight = 1408.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.138913 restraints weight = 901.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.140206 restraints weight = 604.574| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2495 Z= 0.136 Angle : 0.579 6.055 3391 Z= 0.313 Chirality : 0.045 0.153 358 Planarity : 0.005 0.042 445 Dihedral : 5.114 19.236 349 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 5.81 % Allowed : 19.38 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.44), residues: 308 helix: -2.93 (0.75), residues: 31 sheet: 0.34 (0.56), residues: 73 loop : -0.68 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 43 TYR 0.018 0.002 TYR E 495 PHE 0.036 0.002 PHE E 497 TRP 0.011 0.002 TRP A 34 HIS 0.002 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 2490) covalent geometry : angle 0.57745 ( 3381) SS BOND : bond 0.00379 ( 5) SS BOND : angle 1.02645 ( 10) hydrogen bonds : bond 0.03524 ( 62) hydrogen bonds : angle 6.54989 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.085 Fit side-chains REVERT: A 42 GLU cc_start: 0.7210 (tm-30) cc_final: 0.6917 (tm-30) REVERT: E 457 ARG cc_start: 0.8296 (ttt-90) cc_final: 0.7787 (ttt90) outliers start: 15 outliers final: 12 residues processed: 67 average time/residue: 0.0503 time to fit residues: 4.1787 Evaluate side-chains 73 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 518 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 27 optimal weight: 0.1980 chunk 14 optimal weight: 0.4980 chunk 26 optimal weight: 0.0870 chunk 0 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 18 optimal weight: 0.0870 overall best weight: 0.1936 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.143419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.129905 restraints weight = 4422.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.134011 restraints weight = 2385.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.136733 restraints weight = 1429.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.138589 restraints weight = 914.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.139916 restraints weight = 613.453| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2495 Z= 0.155 Angle : 0.590 6.101 3391 Z= 0.319 Chirality : 0.045 0.133 358 Planarity : 0.005 0.041 445 Dihedral : 4.992 15.678 349 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 5.81 % Allowed : 22.09 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.45), residues: 308 helix: -2.86 (0.74), residues: 31 sheet: 0.38 (0.55), residues: 79 loop : -0.74 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 43 TYR 0.013 0.002 TYR E 495 PHE 0.038 0.002 PHE E 497 TRP 0.010 0.002 TRP A 34 HIS 0.002 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 2490) covalent geometry : angle 0.58719 ( 3381) SS BOND : bond 0.00193 ( 5) SS BOND : angle 1.24914 ( 10) hydrogen bonds : bond 0.03504 ( 62) hydrogen bonds : angle 6.57772 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.084 Fit side-chains REVERT: A 42 GLU cc_start: 0.7222 (tm-30) cc_final: 0.6944 (tm-30) REVERT: E 457 ARG cc_start: 0.8168 (ttt-90) cc_final: 0.7699 (ttt90) outliers start: 15 outliers final: 13 residues processed: 67 average time/residue: 0.0449 time to fit residues: 3.6312 Evaluate side-chains 73 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 501 ASN Chi-restraints excluded: chain E residue 518 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 5 optimal weight: 0.0370 chunk 4 optimal weight: 0.0070 chunk 20 optimal weight: 0.6980 chunk 21 optimal weight: 0.1980 chunk 23 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 0.1980 chunk 25 optimal weight: 0.2980 overall best weight: 0.1034 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.145724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.132959 restraints weight = 4290.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.136802 restraints weight = 2345.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.139387 restraints weight = 1406.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.141172 restraints weight = 895.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.142411 restraints weight = 593.489| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2495 Z= 0.119 Angle : 0.589 6.749 3391 Z= 0.307 Chirality : 0.044 0.153 358 Planarity : 0.005 0.043 445 Dihedral : 4.661 14.598 349 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.65 % Allowed : 23.26 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.44), residues: 308 helix: -3.14 (0.66), residues: 31 sheet: 0.57 (0.58), residues: 72 loop : -0.77 (0.40), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 43 TYR 0.013 0.001 TYR E 495 PHE 0.032 0.002 PHE E 497 TRP 0.012 0.002 TRP E 353 HIS 0.002 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 2490) covalent geometry : angle 0.58759 ( 3381) SS BOND : bond 0.00183 ( 5) SS BOND : angle 1.02384 ( 10) hydrogen bonds : bond 0.03113 ( 62) hydrogen bonds : angle 6.46246 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.095 Fit side-chains REVERT: A 42 GLU cc_start: 0.7216 (tm-30) cc_final: 0.6940 (tm-30) REVERT: E 457 ARG cc_start: 0.8079 (ttt-90) cc_final: 0.7703 (ttt90) outliers start: 12 outliers final: 11 residues processed: 66 average time/residue: 0.0566 time to fit residues: 4.5075 Evaluate side-chains 72 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 518 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 20 optimal weight: 0.1980 chunk 27 optimal weight: 0.4980 chunk 15 optimal weight: 0.2980 chunk 6 optimal weight: 0.0970 chunk 5 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 22 optimal weight: 0.2980 chunk 28 optimal weight: 0.0980 chunk 17 optimal weight: 0.5980 overall best weight: 0.1978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN E 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.144039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.131157 restraints weight = 4331.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.134986 restraints weight = 2391.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.137541 restraints weight = 1444.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.139366 restraints weight = 929.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.140615 restraints weight = 618.101| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2495 Z= 0.155 Angle : 0.605 6.436 3391 Z= 0.321 Chirality : 0.044 0.132 358 Planarity : 0.005 0.041 445 Dihedral : 4.810 14.177 349 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 5.81 % Allowed : 22.48 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.44), residues: 308 helix: -3.00 (0.71), residues: 31 sheet: 0.50 (0.54), residues: 79 loop : -0.80 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 43 TYR 0.012 0.001 TYR E 495 PHE 0.033 0.002 PHE E 497 TRP 0.016 0.002 TRP E 353 HIS 0.003 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 2490) covalent geometry : angle 0.60218 ( 3381) SS BOND : bond 0.00263 ( 5) SS BOND : angle 1.28048 ( 10) hydrogen bonds : bond 0.03415 ( 62) hydrogen bonds : angle 6.51765 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.100 Fit side-chains REVERT: A 42 GLU cc_start: 0.7241 (tm-30) cc_final: 0.6997 (tm-30) REVERT: E 457 ARG cc_start: 0.8076 (ttt-90) cc_final: 0.7795 (ttt90) outliers start: 15 outliers final: 12 residues processed: 71 average time/residue: 0.0590 time to fit residues: 5.0551 Evaluate side-chains 76 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 501 ASN Chi-restraints excluded: chain E residue 518 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 0.0970 chunk 14 optimal weight: 0.8980 chunk 11 optimal weight: 0.0770 chunk 0 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 25 optimal weight: 0.0030 chunk 20 optimal weight: 0.3980 chunk 8 optimal weight: 0.0870 chunk 6 optimal weight: 0.2980 chunk 23 optimal weight: 0.2980 chunk 28 optimal weight: 0.6980 overall best weight: 0.1124 ------------------------------------------------------------------------------- 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 = 0.3945 r_free = 0.3945 target = 0.145911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.133013 restraints weight = 4396.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.136867 restraints weight = 2404.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.139413 restraints weight = 1447.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.141263 restraints weight = 928.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.142493 restraints weight = 615.177| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2495 Z= 0.120 Angle : 0.596 7.269 3391 Z= 0.312 Chirality : 0.044 0.155 358 Planarity : 0.005 0.043 445 Dihedral : 4.531 14.743 349 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 5.04 % Allowed : 22.48 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.44), residues: 308 helix: -2.94 (0.75), residues: 31 sheet: 0.55 (0.56), residues: 72 loop : -0.85 (0.40), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 355 TYR 0.011 0.001 TYR E 495 PHE 0.029 0.002 PHE E 497 TRP 0.016 0.002 TRP E 353 HIS 0.002 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 2490) covalent geometry : angle 0.59303 ( 3381) SS BOND : bond 0.00234 ( 5) SS BOND : angle 1.17964 ( 10) hydrogen bonds : bond 0.03166 ( 62) hydrogen bonds : angle 6.49683 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.097 Fit side-chains REVERT: A 42 GLU cc_start: 0.7237 (tm-30) cc_final: 0.6967 (tm-30) REVERT: E 457 ARG cc_start: 0.8096 (ttt-90) cc_final: 0.7770 (ttt90) outliers start: 13 outliers final: 12 residues processed: 69 average time/residue: 0.0626 time to fit residues: 5.1493 Evaluate side-chains 76 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 501 ASN Chi-restraints excluded: chain E residue 518 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.268 > 50: distance: 21 - 26: 4.505 distance: 26 - 27: 13.942 distance: 27 - 30: 13.564 distance: 28 - 29: 24.052 distance: 28 - 32: 19.639 distance: 30 - 31: 31.283 distance: 32 - 33: 34.882 distance: 32 - 38: 37.391 distance: 33 - 34: 17.785 distance: 33 - 36: 13.287 distance: 34 - 35: 16.091 distance: 34 - 39: 13.287 distance: 35 - 55: 39.079 distance: 36 - 37: 21.137 distance: 37 - 38: 28.593 distance: 39 - 40: 11.319 distance: 40 - 41: 6.731 distance: 40 - 43: 4.107 distance: 41 - 42: 12.241 distance: 41 - 46: 17.236 distance: 43 - 44: 23.873 distance: 43 - 45: 28.821 distance: 46 - 47: 17.093 distance: 47 - 48: 10.556 distance: 47 - 50: 25.076 distance: 48 - 49: 5.073 distance: 48 - 55: 10.875 distance: 50 - 51: 23.864 distance: 51 - 52: 26.287 distance: 52 - 53: 30.734 distance: 53 - 54: 11.022 distance: 55 - 56: 14.301 distance: 56 - 57: 16.602 distance: 56 - 59: 21.155 distance: 57 - 58: 10.934 distance: 57 - 63: 17.286 distance: 59 - 60: 16.287 distance: 60 - 61: 25.959 distance: 60 - 62: 29.382 distance: 64 - 65: 11.014 distance: 64 - 67: 7.302 distance: 65 - 66: 10.750 distance: 65 - 71: 17.871 distance: 67 - 68: 25.815 distance: 68 - 69: 7.269 distance: 68 - 70: 10.924 distance: 71 - 72: 22.318 distance: 72 - 73: 5.680 distance: 72 - 75: 15.511 distance: 73 - 74: 15.166 distance: 73 - 79: 28.694 distance: 75 - 76: 32.526 distance: 76 - 77: 29.953 distance: 76 - 78: 18.264 distance: 79 - 80: 28.563 distance: 80 - 81: 8.544 distance: 80 - 83: 10.633 distance: 81 - 82: 31.605 distance: 81 - 87: 15.153 distance: 83 - 84: 15.261 distance: 84 - 85: 21.174 distance: 84 - 86: 21.611 distance: 87 - 88: 9.695 distance: 88 - 89: 25.810 distance: 89 - 90: 30.942 distance: 89 - 93: 20.276 distance: 91 - 92: 30.433 distance: 92 - 156: 3.850 distance: 93 - 94: 13.518 distance: 94 - 95: 13.447 distance: 94 - 97: 8.267 distance: 95 - 96: 16.910 distance: 95 - 104: 13.102 distance: 97 - 98: 13.106 distance: 98 - 99: 10.200 distance: 98 - 100: 12.198 distance: 99 - 101: 20.806 distance: 100 - 102: 6.572 distance: 102 - 103: 15.755